Heterozygous loss-of-function variants in DOCK4 cause neurodevelopmental delay and microcephaly
Open accessPublished version of a preprint
Abstract
Neurons form the basic anatomical and functional structure of the nervous system, and defects in neuronal differentiation or formation of neurites are associated with various psychiatric and neurodevelopmental disorders. Dynamic changes in the cytoskeleton are essential for this process, which is, inter alia, controlled by the dedicator of cytokinesis 4 ( DOCK4 ) through the activation of RAC1 . Here, we clinically describe 7 individuals (6 males and one female) with variants in DOCK4 and overlapping phenotype of mild to severe global developmental delay. Additional symptoms include coordination or gait abnormalities, microcephaly, nonspecific brain malformations, hypotonia and seizures. Four individuals carry missense variants (three of them detected de novo) and three individuals carry null variants (two of them maternally inherited). Molecular modeling of the heterozygous missense variants suggests that the majority of them affect the globular structure of DOCK4. In vitro functional expression studies in transfected Neuro-2A cells showed that all missense variants impaired neurite outgrowth. Furthermore, Dock4 knockout Neuro-2A cells also exhibited defects in promoting neurite outgrowth. Our results, including clinical, molecular and functional data, suggest that loss-of-function variants in DOCK4 probable cause a variable spectrum of a novel neurodevelopmental disorder with microcephaly.
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Written from the paper’s full text.
TL;DR
Heterozygous loss-of-function and deleterious missense variants in DOCK4 were identified in seven individuals with variable neurodevelopmental delay, microcephaly, and coordination/gait abnormalities. Functional studies in Neuro-2A cells showed impaired neurite outgrowth for all tested missense variants and for Dock4 knockout, supporting DOCK4 as a probable monogenic cause of a neurodevelopmental disorder.
Key findings
- Seven individuals (6 males, 1 female) with heterozygous DOCK4 variants had mild to severe developmental delay; additional features included coordination or gait abnormalities in 5/7, microcephaly in individuals 2 and 7 (OFC Z-scores −3.84 and −2), hypotonia, seizures, and nonspecific brain malformations in 4/6 who underwent MRI.
- Ten clinically relevant DOCK4 variants were identified: seven missense and three null variants; three missense variants were de novo, two null variants were maternally inherited, and ACMG classification yielded three likely pathogenic and seven variants of uncertain significance.
- Structural modeling suggested all missense variants destabilize the DOCK4 fold, and in vitro expression in Neuro-2A cells showed that all tested missense variants significantly impaired neurite outgrowth; Dock4 knockout clones also had significantly shorter total and longest neurites.
- DOCK4 has reduced missense and null variation relative to its 1,966-amino-acid size (pLI = 1, Z score = 1.67), and the authors conclude that heterozygous null and deleterious missense variants in DOCK4 are a probable monogenic cause of a neurodevelopmental disorder with microcephaly.
Methods
- Cohort ascertainment used matchmaking platforms, personal communication, and literature review; genotypic and detailed phenotypic information was obtained for eight individuals, seven of whom were included in the clinical description, and all underwent single or trio exome or genome sequencing with Sanger segregation where appropriate.
- Variants were prioritized by gnomAD v4.0.0 allele frequency below 1%, in silico impact prediction (CADD, REVEL, MutPred2, MetaDome), and candidate gene involvement in neuronal processes; variants were classified using ACMG/ClinGen criteria.
- Functional work used Neuro-2A cells transfected with wild-type or mutant DOCK4-mRFP plasmids, CRISPR-Cas9 Dock4 knockout clones, western blotting, and neurite outgrowth assays after 36 h in differentiation media; statistics used one-way ANOVA with Games–Howell post hoc tests.
Limitations
- The paper states that comprehensive phenotypic information was unavailable for each individual, that using murine Neuro-2A cells to study human variants is a limitation, and that bi-allelic Dock4 knockout cells were analyzed while individuals 5–7 carry heterozygous null variants.
- The paper also states that replication with larger cohorts is necessary and that sex-dependent variable expressivity needs confirmation in a larger cohort with detailed segregation information.
- Evident from the text: the clinical cohort is small (seven individuals), inheritance was unknown or not fully segregating for some cases, and one fetal case with compound heterozygous missense variants was excluded from the clinical description because inheritance was inconsistent with the rest of the cohort.
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Claims the paper makes
17 of 25 cited sources checked · 12 supported · 0 flagged · accuracy not yet measured
- Premisecitation
Loss of DOCK4 function is compensated by overexpression of the DOCK4 interacting partner RAC1, as demonstrated in vitro and in vivo.
“loss of DOCK4 function is compensated by overexpression of the DOCK4 interacting partner RAC1, as demonstrated in vitro (Huang et al. 2019) and in vivo (Guo et al. 2021)”
Quote in the paperSubstantial claim2 of 2 sources checked - Premisecitation
DOCK4 is the only member of the DOCK family that is capable of activating RAP1.
“DOCK4 is the only member of the DOCK family that is capable of activating RAP1 (Yajnik et al. 2003; Shi 2013)”
Quote in the paperNot a substantial claim2 of 2 sources checked- cites Yajnik et al. 2003 source
The Results report that wild-type DOCK4 activated Rap GTPase more than fivefold in transfected cells, supporting its ability to activate Rap1. The paper contrasts DOCK4 with family members associated with Rac signaling, but does not establish that no other DOCK family member can activate Rap1. (LLM, conf=0.88)
Experimental — accuracy not yet measured - cites Shi 2013 source
- Findingcitation
The DOCK4 C terminus (1962KVSQL1966) matches the [RK]-x-[ST] consensus pattern present in a class of known PDZ ligands.
“Although the exact role of individual amino acids within this motif has not been experimentally addressed to date, the DOCK4 C terminus (1962KVSQL1966) matches the [RK]-x-[ST] consensus pattern present in a class of known PDZ ligands (Tonikian et al. 2008).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites Tonikian et al. 2008 source
- Premisecitation
Relevant effects could be concealed by the analysis of differentiated cells, compared to effects that take place mostly during early development, as demonstrated in heterozygous Cux+/− mice.
“relevant effects could be concealed by the analysis of differentiated cells, compared to effects that take place mostly during early development, as demonstrated in heterozygous Cux+/− mice (Oppermann et al. 2023)”
Quote in the paperSubstantial claim1 of 1 sources checked- cites Oppermann et al. 2023 source
The Results section (Analysis of Cux1 heterozygous mice; page unavailable) reports reduced CUX1 immunoreactivity at P10 but no significant difference at P30, supporting the possibility that a later-stage analysis could miss an earlier difference. It does not establish that relevant effects occur mostly during early development or that analysis of differentiated cells generally conceals them; western blots found reduced p200 CUX1 at all tested ages. (LLM, conf=0.83)
Experimental — accuracy not yet measured
- Findingown data
Dock4 knockout Neuro-2A cells (clones ko1, ko2a and ko2b) had significantly shorter neurites (total and longest) compared to control and wild-type cells.
“The neurite outgrowth assay demonstrated that the different knockout clones ko1, ko2a and ko2b cells had significant shorter neurites (total and longest neurite length) compared to control and wild-type cells (Fig. 4).”
Quote in the paperSubstantial claim
- Findingown data
The missense variants p.Thr982Ile, p.Met1044Thr and p.Ile1067Thr were absent from gnomAD.
“The missense variants p.Thr982Ile, p.Met1044Thr and p.Ile1067Thr were absent from gnomAD.”
Quote in the paperSubstantial claim - Findingown data
Several small parts of DOCK4 seem to be highly depleted of missense variants in the general population.
“Only several small parts of DOCK4 seem to be highly depleted of missense variants in the general population (Fig. 1A).”
Quote in the paperNot a substantial claim - Findingown data
Three individuals had a de novo missense variant in DOCK4.
“In three individuals, we detected a de novo missense variant.”
Quote in the paperNot a substantial claim - Findingown data
Similar steric problems emerge from the longer methionine sidechain in p.Val420Met and the β-branched threonine sidechain in p.Met1044Thr.
“Similar steric problems emerge from the longer methionine sidechain in the p.Val420Met and the β-branched threonine sidechain in the p.Met1044Thr variant.”
Quote in the paperNot a substantial claim - Findingown data
Ten clinically relevant variants in DOCK4 were identified: seven missense and three null variants.
“In total, we identified ten clinical relevant variants in DOCK4: seven missense and three null variants (Fig. 1A).”
Quote in the paperSubstantial claim - Findingown data
The missense variants from individuals 2 and 3 are predicted to be deleterious by CADD and MutPred2.
“The missense variants from individuals 2 and 3 are predicted to be deleterious by CADD and MutPred2 (Table S1).”
Quote in the paperNot a substantial claim - Findingown data
The gnomAD variant p.Pro1733Ala was indistinguishable from wild type in the neurite outgrowth assay.
“Moreover, the gnomAD variant p.Pro1733Ala was indistinguishable from the wild type, supporting its nonpathogenic nature”
Quote in the paperSubstantial claim - Findingown data
Structural modeling of the variants in the globular domain reveals that all of them cause a destabilization of the DOCK4 fold.
“Structural modeling of the variants in the globular domain reveals that all of them cause a destabilization of the DOCK4 fold.”
Quote in the paperSubstantial claim - Findingown data
Muscular hypotonia was present in individuals 2, 4 and 7.
“Other neurological symptoms were muscular hypotonia (individuals 2, 4 and 7) and different types of seizures.”
Quote in the paperNot a substantial claim - Findingown data
Seven individuals with heterozygous rare variants in DOCK4 were identified and clinically described.
“Here, we clinically describe 7 individuals (6 males and one female) with variants in DOCK4 and overlapping phenotype of mild to severe global developmental delay.”
- Also stated in: § Clinical description · plain
“In this study, we report on seven individuals with heterozygous rare variants in DOCK4.”
Quote in the paperSubstantial claim - Also stated in: § Clinical description · plain
- Findingown data
Overexpression of wild-type DOCK4 promoted neurite formation, as demonstrated by significantly longer neurites compared to cells transfected with the empty vector alone.
“As expected, overexpression of wild-type DOCK4 promoted neurite formation, as demonstrated by significantly longer neurites compared to cells transfected with the empty vector alone (Fig. 3).”
Quote in the paperSubstantial claim - Findingown data
Microcephaly was present in individuals 2 (OFC 43.3 cm; Z-score -3.84) and 7 (OFC 48 cm; Z-score -2).
“Additional findings include microcephaly in individuals 2 (OFC: 43.3 cm; Z-score: -3.84) and 7 (OFC: 48 cm; Z-score: -2).”
Quote in the paperSubstantial claim - Findingown data
No clustering of disease-causing missense variants in a specific region of DOCK4 was observed.
“A clustering of disease-causing missense variants in a specific region of DOCK4 was not observed.”
Quote in the paperNot a substantial claim - Findingown data
The positive controls p.Arg853Leu and p.Pro1718Leu resulted in significantly reduced neurite outgrowth.
“and the positive controls p.Arg853Leu and p.Pro1718Leu resulted in a significantly reduced neurite outgrowth.”
Quote in the paperSubstantial claim - Findingown data
The missense variants are located in the proline-rich C-terminal end, in the DHR-1 and proximal of the DHR-2 domain.
“The missense variants are located in the proline-rich C-terminal end, in the DHR-1 and proximal of the DHR-2 domain (Fig. 1).”
Quote in the paperNot a substantial claim - Findingown data
All seven individuals presented with developmental delay of variable severity, ranging from mild to severe.
“All individuals presented with DD of variable severity, ranging between mild (individuals 2, 3, 5 and 6), moderate (individuals 1 and 7) and severe (individual 4).”
Quote in the paperSubstantial claim - Findingown data
The p.Thr982Ile exchange induces steric clashes with Leu923 due to the longer isoleucine sidechain.
“The p.Thr982Ile exchange induces steric clashes with Leu923 due to the longer isoleucine sidechain present in the variant (Fig. 2B, C).”
Quote in the paperNot a substantial claim - Findingown data
Cognitive impairment in the cohort ranged from learning difficulties with no intellectual disability to mild and moderate intellectual disability.
“Cognitive impairment was highly variable, ranging from learning difficulties with no ID (individuals 3 and 6) to mild (individuals 2 and 5) and moderate ID (individuals 1 and 4).”
Quote in the paperNot a substantial claim - Findingown data
The destabilizing variants can be divided into two categories: introduction of steric clashes and loss of hydrophobic interactions.
“Depending on the molecular origin of destabilization, the variants can roughly be divided into two categories: introduction of steric clashes and loss of hydrophobic interactions.”
Quote in the paperNot a substantial claim - Findingown data
A similar loss of hydrophobic interactions is observed for the p.Pro253Leu and p.Val1042Ala variants.
“A similar loss of hydrophobic interactions is observed for the p.Pro253Leu and p.Val1042Ala variants.”
Quote in the paperNot a substantial claim - Findingown data
Five out of seven individuals had coordination or gait abnormalities.
“Different coordination or gait abnormalities were reported in five out of seven individuals.”
Quote in the paperNot a substantial claim - Findingnone given
The variant p.Lys1962Asn is located in the nonglobular C terminus of DOCK4.
“The variant p.Lys1962Asn is located in the nonglobular C terminus of DOCK4.”
Quote in the paperSubstantial claim - Findingown data
The inherited null variants p.Arg298*, p.Arg924* and p.Asp1304Thrfs*27 were detected in gnomAD with very low frequencies (0.00014%, 0.000136% and 0.0001%, respectively).
“The inherited null variants were also detected in gnomAD with a very low frequency (p.Arg298*: 0.00014%; p.Arg924*: 0.000136%; p.Asp1304Thrfs*27: 0.0001%).”
Quote in the paperSubstantial claim - Study design and conductown data
Dock4 knockout was confirmed by DNA sequencing and western blotting.
“Dock4 knockout was confirmed by DNA sequencing and western blot (Fig. S1).”
Quote in the paperSubstantial claim - Interpretationown data
A gain-of-function mechanism of missense variants is unlikely because overexpression of wild-type DOCK4 results in increased neurite outgrowth capabilities and not the opposite.
“A gain-of-function mechanism of missense variants is unlikely because overexpression of wild-type DOCK4 results in increased neurite outgrowth capabilities and not the opposite (Fig. 3)”
Quote in the paperSubstantial claim - Interpretationown data
Null variants and deleterious missense variants in DOCK4 lead to impaired function in promoting neurite growth.
“Taken together, our experiments demonstrated that null variants and deleterious missense variants lead to impaired function in promoting neurite growth, supporting the association of DD/ID and the variants of the individuals of the present cohort.”
Quote in the paperSubstantial claim- The authors state this as an assumption: The three identified null variants lead to mRNA degradation by nonsense-mediated mRNA decay, causing haploinsufficiency.
- Interpretationreasoning
Replacement of the positively charged lysine by an uncharged asparagine in p.Lys1962Asn leads to decreased affinity of DOCK4 for harmonin and/or other PDZ domain-containing proteins.
“This observation suggests that replacement of the positively charged lysine by an uncharged asparagine in the p.Lys1962Asn variant leads to a decreased affinity of DOCK4 for harmonin and/or other PDZ domain-containing proteins.”
Quote in the paperSubstantial claim - Interpretationown data
Loss-of-function variants in DOCK4 probably cause a variable spectrum of a novel neurodevelopmental disorder with microcephaly.
“Our results, including clinical, molecular and functional data, suggest that loss-of-function variants in DOCK4 probable cause a variable spectrum of a novel neurodevelopmental disorder with microcephaly.”
Quote in the paperSubstantial claim- The authors state this as an assumption: The three identified null variants lead to mRNA degradation by nonsense-mediated mRNA decay, causing haploinsufficiency.
- Interpretationreasoning
Heterozygous null variants and deleterious missense variants in DOCK4 are a probable monogenetic cause of an NDD with microcephaly.
“prompt us to add heterozygous null variants and deleterious missense variants in DOCK4 as a probable monogenetic cause of an NDD with microcephaly”
- Also stated in: § Discussion · hedged
“In summary, the overlapping phenotype of seven Individuals, the structural modeling, the role of DOCK4 in the central nervous system and the proven impact of the variants on neuronal outgrowth prompt us to add heterozygous null variants and deleterious missense variants in DOCK4 as a probable monogenetic cause of an NDD with microcephaly.”
Quote in the paperSubstantial claim - Also stated in: § Discussion · hedged
- May combine two claims. 15
- Classified as probably not a substantial claim. 27
May combine two claims.
FindingcitationDOCK4 has a reduced amount of missense and null variants compared to its size of 1,966 amino acids (pLI = 1, Z score = 1.67) in a population without severe, early-onset phenotypes, indicating a mild constraint.
“Based on gnomAD (Karczewski et al. 2020), DOCK4 has a reduced amount of missense and null variants compared to its size of 1,966 amino acids (pLI = 1, Z score = 1.67) in a population without severe, early-onset phenotypes, indicating a mild constraint.”
Quote in the paperSubstantial claim1 of 1 sources checked- cites Karczewski et al. 2020 source
The LoF intolerance of human genes section describes using gnomAD to identify genes depleted of predicted loss-of-function variants, and Additional information says individuals with severe pediatric disease were excluded. However, the passages found do not give DOCK4’s variant counts, protein length, pLI, or missense Z score, so they do not establish the claimed mild constraint for that gene. (LLM, conf=0.85)
Experimental — accuracy not yet measured
Classified as probably not a substantial claim.
PremisecitationDHR2 is responsible for binding and activation of RAC1.
“the latter is responsible for binding and activation of RAC1 (Shi 2013).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites Shi 2013 source
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationInteraction of the proline-rich C terminus of DOCK4 with cortactin is important for dendritic spine formation.
“and interaction with the proline-rich C terminus with cortactin for dendritic spine formation (Ueda et al. 2013).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites Ueda et al. 2013 source
Classified as probably not a substantial claim.
Study design and conductcitationAll variants in DOCK4 were classified according to ACMG criteria and ClinGen recommendations.
“All variants in DOCK4 are described with regard to the human reference genome version GRCh38 and to the transcript NM_014705.4 and have been classified according to the criteria of the American College of Medical Genetics (ACMG) (Richards et al. 2015) and the recommendations of the Sequence Variant Interpretation Working Group (ClinGen).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites Richards et al. 2015 source
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationBi-allelic null variants in DOCK6 cause Adams-Oliver syndrome.
“bi-allelic null variants in DOCK6 (MIM: #614,219) and DOCK7 (MIM: #615,859), members of the dedicator of cytokinesis (DOCK) family, are a cause for the Adams–Oliver syndrome (Sukalo et al. 2015) and epileptic encephalopathy (Perrault et al. 2014), respectively.”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites Sukalo et al. 2015 source
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationSeveral disease-causing genes remain undiscovered.
“Although the rate of discovery of new rare disease–gene associations has declined in recent years (Ehrhart et al. 2021), several disease-causing genes remain undiscovered, as demonstrated by a recent analysis of the X chromosome (Leitão et al. 2022).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites Leitão et al. 2022 source
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationWiltrout et al. reported three individuals with developmental delay, hypotonia, coordination or gait abnormalities and bi-allelic variants in DOCK3.
“Furthermore, Wiltrout et al. reported three individuals with DD, hypotonia, coordination or gait abnormalities and bi-allelic variants in DOCK3 (MIM: #618,292) (Wiltrout et al. 2019).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites Wiltrout et al. 2019 source
Classified as probably not a substantial claim. May combine two claims.
Study design and conductcitationAll variants were prioritized considering allele frequency in gnomAD v4.0.0 below 1%, impact on protein function via different in silico programs, and involvement of candidate genes in neuronal processes.
“All variants were prioritized considering allele frequency in gnomAD v4.0.0 (Karczewski et al. 2020) below 1%, impact on protein function via different in silico programs (CADD (Rentzsch et al. 2021), REVEL (Ioannidis et al. 2016), MutPred2 (Pejaver et al. 2020) and Metadome (Wiel et al. 2019)) and involvement of candidate genes in neuronal processes.”
Quote in the paperSubstantial claim2 of 3 sources checked- cites Karczewski et al. 2020 source
The Discussion identifies gnomAD as a resource for allele-frequency estimates, supporting its use for that purpose. But Data availability specifies that this paper provides gnomAD 2.1.1, not the cited v4.0.0. The below-1% cutoff is the citing authors’ prioritization criterion, not a finding attributed to this source. (LLM, conf=0.90)
Experimental — accuracy not yet measured - cites Rentzsch et al. 2021 source
- cites Ioannidis et al. 2016 source
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationThe approach of using Neuro-2A cells to validate the impact of missense variants associated with human disorders is still being used successfully in recent studies.
“this approach is still being used successfully in recent studies to validate the impact of missense variants associated with human disorders (Cioclu et al. 2023)”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites Cioclu et al. 2023 source
The Methods (page unavailable) and Results, ‘Functional Analysis of KCNT2 Channels Carrying Disease-Causing Variants’ (page unavailable), describe testing disorder-associated variants in cultured cells and finding functional effects. But the cells were HEK-293 and SH-SY5Y, not Neuro-2A, so the paper does not support the claim about continued use of Neuro-2A cells. (LLM, conf=0.86)
Experimental — accuracy not yet measured
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationThe proline-rich C terminus of DOCK4 is required for dendritic spine formation via interaction with cortactin.
“Ueda et al. (2013) demonstrated that proline-rich C terminus of DOCK4 is required for dendritic spine formation via interaction with cortactin”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites Ueda et al. (2013) source
May combine two claims.
Findingown dataSeizures occurred in the cohort: individual 1 had focal to bilateral tonic-clonic seizures, and individual 7 had an abnormal EEG consistent with a focal onset seizure.
“Individual 1 had focal to bilateral tonic–clonic seizures, and individual 7 had an abnormal EEG that is consistent with a focal onset seizure.”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataBehavioral abnormalities included autism or autistic behavior in individuals 4 and 5, and attention disorder and anxiety in individual 6.
“Behavioral abnormalities were less common, with a diagnosis of autism or autistic behavior in individuals 4 and 5, and attention disorder and anxiety in individual 6.”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataBoth Dock4 knockout and the missense variants investigated resulted in impaired function in promoting neurite outgrowth in Neuro-2A cells.
“both Dock4 knockout and the missense variants investigated resulted in impaired function in promoting neurite outgrowth in Neuro-2A cells”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataTwo null variants in DOCK4 were maternally inherited, and the inheritance of the null variant in individual 6 is unknown.
“Two null variants were maternally inherited, and the inheritance of the null variant of individual 6 is unknown (Fig. 1B).”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataSix individuals underwent MRI and four had nonspecific brain abnormalities.
“Six individuals underwent MRI and four had nonspecific brain abnormalities.”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataIn p.Ile1067Thr, the isoleucine is replaced by a shorter threonine, resulting in a loss of hydrophobic interactions with Val1106 and Lys1109.
“In the p.Ile1067Thr variant, the isoleucine is replaced by a shorter threonine. This results in a loss of hydrophobic interactions with Val1106 and Lys1109 (Fig. 2D, E).”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataThe variants p.Lys1962Asn and p.Val1042Ala were detected in gnomAD once, and p.Pro253Leu and p.Val420Met had allele frequencies of 0.061% and 0.00186%, respectively.
“The variants p.Lys1962Asn and p.Val1042Ala were detected in gnomAD once, and the two inherited missense variants p.Pro253Leu and p.Val420Met (detected compound heterozygous with the variant p.Val1042Ala) were observed with an allele frequency of 0.061% and 0.00186% in gnomAD, respectively.”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataThe AlphaFold-2 model of DOCK4 is reliable for residues 1-1587, whereas low confidence scores for residues 1588-1966 suggest that the C terminus is disordered and lacks a defined three-dimensional structure.
“Inspection of the AlphaFold scores indicates a reliable model for residues 1–1587, whereas the low confidence scores for residues 1588–1966 suggest that the C terminus is disordered and lacks a defined three-dimensional structure.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
Findingown dataMinor facial dysmorphisms were reported for four individuals (2, 4, 5 and 7), with no apparent shared facial gestalt.
“Although minor facial dysmorphisms have been reported for four individuals (individuals 2, 4, 5 and 7), there was no apparent shared facial gestalt (Table S1).”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Findingown dataTwo compound heterozygous missense variants in DOCK4 were identified in a fetus with microcephaly, rhombencephalosynapsis and microlissencephaly.
“It should be noted that we also identified two compound heterozygous missense variants in a fetus with microcephaly, rhombencephalosynapsis and microlissencephaly (Table S1).”
Quote in the paperNot a substantial claimMay combine two claims.
Interpretationown dataNo functional role can be assigned to Pro1733, suggesting that the p.Pro1733Ala exchange does not critically affect DOCK4 function.
“In contrast, no functional role can be assigned to Pro1733, suggesting that the p.Pro1733Ala exchange (rs150569245, detected with a frequency of 1.163% in gnomAD) does not critically affect DOCK4 function.”
Quote in the paperNot a substantial claimClassified as probably not a substantial claim.
PremisecitationDisease-causing variants in genes involved in cytoskeletal regulation, such as RHOA, CDC42 and RAC1, are associated with a neurodevelopmental disorder.
“Disease-causing variants in genes that are involved in this process, such as RHOA (MIM: #618,727), CDC42 (MIM: #616,737) and RAC1 (MIM: #617,751), are associated with a NDD.”
Quote in the paperSubstantial claim0 of 3 sources checked- cites MIM: #618,727
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- cites MIM: #616,737
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- cites MIM: #617,751
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
Probably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductnone givenAll sequences were verified by Sanger sequencing.
“All sequences were verified by Sanger sequencing.”
Quote in the paperNot a substantial claimClassified as probably not a substantial claim.
PremisecitationThe formation and function of dendrites and neurites are highly dependent on dynamic changes in the cytoskeleton that are regulated by small GTPases.
“The formation and function of dendrites and neurites are highly dependent on dynamic changes in the cytoskeleton that are regulated by small GTPases (Nimchinsky et al. 2002).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Nimchinsky et al. 2002 source
Classified as probably not a substantial claim.
PremisecitationDOCK4-dependent RAC1 activation is important for neurite differentiation.
“The DOCK4-dependent RAC1 activation has been reported as important for neurite differentiation (Xiao et al. 2013)”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Xiao et al. 2013 source
Probably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductnone givenSanger sequencing was used for segregation analysis where appropriate.
“Maternity and paternity were confirmed for all individuals, and Sanger sequencing was used for segregation analysis where appropriate.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductown dataAt least 70 cells per group were analyzed in each neurite outgrowth experiment.
“At least 70 cells/group were analyzed in each experiment.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductown dataThe result of each neurite outgrowth assay per group was confirmed by at least two individual experiments.
“The result of each assay per group was confirmed by at least two individual experiments, and representative data are shown.”
Quote in the paperNot a substantial claimMay combine two claims.
InterpretationcitationThe paternally inherited variant p.Pro253Leu was detected together with the de novo variant p.Met1044Thr in individual 2; phasing was not possible, but it is more likely that the de novo variant is also located on the paternal allele (in cis).
“It should be noted that the paternally inherited variant p.Pro253Leu was detected together with the de novo variant p.Met1044Thr in individual 2. Unfortunately, phasing of the de novo variant was not possible, but it is more likely that this variant is also located on the paternal allele (i.e., in cis) (Jónsson et al. 2017).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Jónsson et al. 2017 source
Classified as probably not a substantial claim.
Premisenone givenDysregulation of guanine nucleotide exchange factors that regulate RAC1 activity is associated with developmental delay/intellectual disability.
“In addition, dysregulation of guanine nucleotide exchange factors that regulate RAC1 activity is also associated with DD/ID.”
Quote in the paperSubstantial claimMay combine two claims.
Interpretationown dataIn silico structural modeling suggests a loss-of-function mechanism for the missense variants, comparable to the mechanism for the null variants.
“our in silico structural modeling suggests a loss-of-function mechanism for the missense variants, which is a comparable mechanism for the null variants”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationBi-allelic null variants in DOCK7 cause epileptic encephalopathy.
“bi-allelic null variants in DOCK6 (MIM: #614,219) and DOCK7 (MIM: #615,859), members of the dedicator of cytokinesis (DOCK) family, are a cause for the Adams–Oliver syndrome (Sukalo et al. 2015) and epileptic encephalopathy (Perrault et al. 2014), respectively.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Perrault et al. 2014 source
Classified as probably not a substantial claim.
Study design and conductnone givenMaternity and paternity were confirmed for all individuals.
“Maternity and paternity were confirmed for all individuals, and Sanger sequencing was used for segregation analysis where appropriate.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
Study design and conductreasoningSHSY5Y is derived from neuroblastoma and is therefore also a limitation to investigate NDD.
“this cell line is also derived from neuroblastoma and is therefore also a limitation to investigate NDD”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Premisenone givenThe human DOCK4 sequence is highly conserved, with 98.18% protein sequence similarity to murine Dock4.
“we used the human DOCK4 sequence, which is highly conserved (98.18%% protein sequence similarity to murine Dock4)”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductreasoningThe use of a murine neuroblastoma cell line (Neuro-2A) to study the effect of variants identified in humans is a limitation.
“the use of a murine neuroblastoma cell line (Neuro-2A) to study the effect of variants identified in humans is also a limitation”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductreasoningAnother limitation of the present study is the analysis of bi-allelic Dock4 KO cells, while individuals 5-7 carry heterozygous null variants.
“Another limitation of the present study is the analysis of bi-allelic Dock4 KO cells, while individuals 5–7 carry heterozygous null variants”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductnone givenA limitation of the study is the unavailability of comprehensive phenotypic information for each individual.
“A limitation of the study is the unavailability of comprehensive phenotypic information for each individual”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductreasoningThe genetic background of the murine Neuro-2A cell line is different from human.
“the genetic background is indeed different”
Quote in the paperNot a substantial claim
The authors state this as an assumption.
The three identified null variants lead to mRNA degradation by nonsense-mediated mRNA decay, causing haploinsufficiency.
“For the three identified null variants, it can be assumed that the mRNA is degraded by nonsense-mediated mRNA decay (Lindeboom et al. 2016) causing haploinsuffuciency.”
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
Each contradiction between two passages listed here was confirmed by an independent check.
Control variant is named both p.Arg853Leu and p.Arg853His
MinorThe Results text calls the positive-control variant p.Arg853Leu, while the Fig. 3 caption calls it p.Arg853His.
“the positive controls p.Arg853Leu and p.Pro1718Leu resulted in a significantly reduced neurite outgrowth.”
“the positive controls p.Arg853His and p.Pro1718Leu”
Variant of unknown inheritance is called inherited
MinorThe genetic findings include p.Arg924* among the inherited null variants, although Table 1 lists its inheritance as unknown (not maternal).
“The inherited null variants were also detected in gnomAD with a very low frequency (p.Arg298*: 0.00014%; p.Arg924*: 0.000136%; p.Asp1304Thrfs*27: 0.0001%).”
“| 6 | c.2770C > T; p.Arg924* | unknown (not maternal) | F | 20 y | Y, mild | N | | N | Attention disorder, anxiety, global learning difficulties, ophthalmologic abnormalities |”
Individual 5's microcephaly is omitted from the clinical description
MinorThe clinical description identifies individuals 2 and 7 as having microcephaly, whereas Table 1 marks individual 5 as having it.
“Additional findings include microcephaly in individuals 2 (OFC: 43.3 cm; Z-score: -3.84) and 7 (OFC: 48 cm; Z-score: -2).”
“| 5 | c.892C > T; p.Arg298* | maternal | M | 6 y | Y, mild | Y, mild | Y | N | Facial dysmorphism, ASD |”
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MethodHighly accurate protein structure prediction with AlphaFold
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“According to ACMG criteria (Richards et al. 2015), three variants can be classified as likely pathogenic and seven as variants of uncertain significance (Table S1).”
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MethodThe mutational constraint spectrum quantified from variation in 141,456 humans
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“The structural analysis of DOCK4 was based on a model available in the AlphaFold Protein Structure Database at: https:// alpha fold. ebi. ac. uk/ entry/ Q8N1I0 (Jumper et al. 2021; Varadi et al. 2022).”
MethodPhosphoSitePlus, 2014: mutations, PTMs and recalibrations
Hornbeck, P. V., Zhang, B., Murray, B., Kornhauser, J. M., Latham, V. M., & Skrzypek, E. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1267 · Cited by 3,243 · see citing works
REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants
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“0.0 (Karczewski et al. 2020) below 1%, impact on protein function via different in silico programs (CADD (Rentzsch et al. 2021), REVEL (Ioannidis et al. 2016), MutPred2 (Pejaver et al. 2020) and Metadome (Wiel et al. 2019)) and involvement of candidate genes in neuronal processes.”
BackgroundInfluentialDesign and validation of a tool for neurite tracing and analysis in fluorescence microscopy images
Meijering, E. H. W., Jacob, M., Sarria, J. ‐. F., Steiner, P., Hirling, H., & Unser, M. A. (2004) · Cytometry Part A · doi:10.1002/cyto.a.20022 · Cited by 1,611 · cited 1× · see citing works
“Neurite length was determined after 36 h in differentiation media by using NeuronJ (Meijering et al. 2004) implemented in ImageJ.”
MethodGeneMatcher: a matching tool for connecting investigators with an interest in the same gene.
Sobreira, N., Schiettecatte, F., Valle, D., & Hamosh, A. (2015) · Human Mutation · doi:10.1002/humu.22844 · Cited by 1,529 · cited 1× · see citing works
“By using match making platforms (Sobreira et al. 2015), personal communication and a literature review, nine different families and 17 individuals from the literature (for further details see Supplemental Information) with potential causative DOCK4 variants were assessed.”
BackgroundStructure and function of dendritic spines
Nimchinsky, E. A., Sabatini, B. L., & Svoboda, K. (2002) · Annual Review of Physiology · doi:10.1146/annurev.physiol.64.081501.160008 · Cited by 1,208 · cited 1× · see citing works
“The formation and function of dendrites and neurites are highly dependent on dynamic changes in the cytoskeleton that are regulated by small GTPases (Nimchinsky et al. 2002).”
BackgroundInferring the molecular and phenotypic impact of amino acid variants with MutPred2
Pejaver, V., Urresti, J., Lugo-Martinez, J., Pagel, K. A., Lin, G. N., Nam, H.-J., Mort, M., Cooper, D. N., Sebat, J., Iakoucheva, L. M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-19669-x · Cited by 923 · cited 2× · see citing works
“0.0 (Karczewski et al. 2020) below 1%, impact on protein function via different in silico programs (CADD (Rentzsch et al. 2021), REVEL (Ioannidis et al. 2016), MutPred2 (Pejaver et al. 2020) and Metadome (Wiel et al. 2019)) and involvement of candidate genes in neuronal processes.”
BackgroundInfluentialRentzsch, P., Schubach, M., Shendure, J., & Kircher, M. (2021) · Genome Medicine · doi:10.1186/s13073-021-00835-9 · Cited by 640 · cited 1× · see citing works
“0.0 (Karczewski et al. 2020) below 1%, impact on protein function via different in silico programs (CADD (Rentzsch et al. 2021), REVEL (Ioannidis et al. 2016), MutPred2 (Pejaver et al. 2020) and Metadome (Wiel et al. 2019)) and involvement of candidate genes in neuronal processes.”
BackgroundInfluentialStrande, N. T., Riggs, E. R., Buchanan, A. H., Ceyhan‐Birsoy, O., DiStefano, M. T., Dwight, S. S., Goldstein, J., Ghosh, R., Seifert, B. A., Sneddon, T. P., et al. (2017) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2017.04.015 · Cited by 587 · see citing works
Parental influence on human germline de novo mutations in 1,548 trios from Iceland
Jónsson, H., Sulem, P., Kehr, B., Kristmundsdottir, S., Zink, F., Hjartarson, E., Hardarson, M. T., Hjorleifsson, K. E., Eggertsson, H. P., Gudjonsson, S. A., et al. (2017) · Nature · doi:10.1038/nature24018 · Cited by 561 · cited 2× · see citing works
“Unfortunately, phasing of the de novo variant was not possible, but it is more likely that this variant is also located on the paternal allele (i.e., in cis ) (Jónsson et al. 2017).”
BackgroundThe rules and impact of nonsense-mediated mRNA decay in human cancers
Lindeboom, R. G. H., Supek, F., & Lehner, B. (2016) · Nature Genetics · doi:10.1038/ng.3664 · Cited by 549 · cited 1× · see citing works
“For the three identified null variants, it can be assumed that the mRNA is degraded by nonsense-mediated mRNA decay (Lindeboom et al. 2016) causing haploinsuffuciency.”
BackgroundA Specificity Map for the PDZ Domain Family
Tonikian, R., Zhang, Y., Sazinsky, S. L., Currell, B., Yeh, J.-H., Reva, B., Held, H. A., Appleton, B. A., Evangelista, M., Wu, Y., et al. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060239 · Cited by 476 · cited 1× · see citing works
“Although the exact role of individual amino acids within this motif has not been experimentally addressed to date, the DOCK4 C terminus ( 1962 KVSQL 1966 ) matches the [RK]-x-[ST] consensus pattern present in a class of known PDZ ligands (Tonikian et al. 2008).”
BackgroundKochinke, K., Zweier, C., Nijhof, B., Fencková, M., Čížek, P., Honti, F., Keerthikumar, S., Oortveld, M. A. W., Kleefstra, T., Kramer, J. M., et al. (2016) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2015.11.024 · Cited by 316 · cited 1× · see citing works
“According to the SysNDD (Kochinke et al. 2016) database, pathogenic variants in 1780 (gene statistics from October 26, 2023) different genes are currently established as causes of diverse neurodevelopmental disorders (NDD).”
MethodWiel, L., Baakman, C. A. B., Gilissen, D., Veltman, J. A., Vriend, G., & Gilissen, C. (2019) · Human Mutation · doi:10.1002/humu.23798 · Cited by 262 · cited 1× · see citing works
“0.0 (Karczewski et al. 2020) below 1%, impact on protein function via different in silico programs (CADD (Rentzsch et al. 2021), REVEL (Ioannidis et al. 2016), MutPred2 (Pejaver et al. 2020) and Metadome (Wiel et al. 2019)) and involvement of candidate genes in neuronal processes.”
InfluentialSheridan, E. G., Wright, J., Small, N., Corry, P. C., Oddie, S., Whibley, C., Petherick, E., Malik, T., Pawson, N., McKinney, P. A., et al. (2013) · The Lancet · doi:10.1016/s0140-6736(13)61132-0 · Cited by 255 · cited 1× · see citing works
“Global developmental delay (DD), often leading to intellectual disability (ID), has a prevalence of about 2% and is among the most frequent indications for genetic testing (Sheridan et al. 2013).”
BackgroundDOCK4, a GTPase activator, is disrupted during tumorigenesis.
Yajnik, V., Paulding, C., Sordella, R., McClatchey, A. I., Saito, M., Wahrer, D. C. R., Reynolds, P., Bell, D. W., Lake, R., van den Heuvel, S., et al. (2003) · Cell · doi:10.1016/s0092-8674(03)00155-7 · Cited by 230 · cited 2× · see citing works
“Furthermore, DOCK4 is the only member of the DOCK family that is capable of activating RAP1 (Yajnik et al. 2003; Shi 2013).”
BackgroundMethodThe Eukaryotic Linear Motif resource: 2022 release
Kumar, M., Michael, S., Alvarado-Valverde, J., Mészáros, B., Sámano-Sánchez, H., Zeke, A., Dobson, L., Lazar, T., Örd, M., Nagpal, A., et al. (2021) · Nucleic Acids Res. · doi:10.1093/nar/gkab975 · Cited by 227 · see citing works
Pagnamenta, A. T., Bacchelli, E., de Jonge, M. V., Mirza, G., Scerri, T. S., Minopoli, F., Chiocchetti, A., Ludwig, K. U., Hoffmann, P., Paracchini, S., et al. (2010) · Biological Psychiatry · doi:10.1016/j.biopsych.2010.02.002 · Cited by 139 · cited 1× · see citing works
“Pagnamenta et al .”
Human and mouse essentiality screens as a resource for disease gene discovery
Cacheiro, P., Muñoz‐Fuentes, V., Murray, S. A., Dickinson, M. E., Bućan, M., Nutter, L. M. J., Peterson, K. A., Haselimashhadi, H., Flenniken, A. M., Morgan, H., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-14284-2 · Cited by 105 · cited 1× · see citing works
“Interestingly, Dock4 knockout in mice leads to early embryonic lethality (Abraham et al. 2015), which is frequently observed in NDD genes with an autosomal dominant mode of inheritance (Cacheiro et al. 2020).”
BackgroundGuo, D., Peng, Y., Wang, L., Sun, X., Wang, X., Liang, C., Yang, X., Li, S., Xu, J., Ye, W.-C., et al. (2021) · Molecular Psychiatry · doi:10.1038/s41380-019-0472-7 · Cited by 102 · cited 3× · see citing works
“…to the recommendations of ClinGen (Strande et al. 2017), including the experimental evidence of the published cell culture studies (Ueda et al. 1993; Huang et al. 2019), mouse studies (Guo et al. 2021) and the cohort of the present study, would result in supporting evidence of moderate level.”
BackgroundInfluentialFront Cover, Volume 40, Issue 8
Wiel, L., Baakman, C. A. B., Gilissen, D., Veltman, J. A., Vriend, G., & Gilissen, C. (2019) · Human Mutation · doi:10.1002/humu.23892 · Cited by 85 · cited 1× · see citing works
“0.0 (Karczewski et al. 2020) below 1%, impact on protein function via different in silico programs (CADD (Rentzsch et al. 2021), REVEL (Ioannidis et al. 2016), MutPred2 (Pejaver et al. 2020) and Metadome (Wiel et al. 2019)) and involvement of candidate genes in neuronal processes.”
BackgroundInfluentialDock protein family in brain development and neurological disease
Shi, L. (2013) · Communicative & Integrative Biology · doi:10.4161/cib.26839 · Cited by 83 · see citing works
Abraham, S., Scarcia, M., Bagshaw, R. D., McMahon, K., Grant, G., Harvey, T. J., Yeo, M., Esteves, F., Thygesen, H. H., Jones, P. F., et al. (2015) · Nature Communications · doi:10.1038/ncomms8286 · Cited by 79 · cited 2× · see citing works
“In contrast, no functional role can be assigned to Pro1733, suggesting that the p.Pro1733Ala exchange (rs150569245, detected with a frequency of 1.163% in gnomAD) does not critically affect DOCK4 function.”
BackgroundInfluentialXiao, Y., Peng, Y., Wan, J., Tang, G., Chen, Y., Tang, J., Ye, W.-C., Ip, N. Y., & Shi, L. (2013) · Journal of Biological Chemistry · doi:10.1074/jbc.m113.458612 · Cited by 71 · cited 2× · see citing works
“The DOCK4 -dependent RAC1 activation has been reported as important for neurite differentiation (Xiao et al. 2013) and interaction with the proline-rich C terminus with cortactin for dendritic spine formation (Ueda et al. 2013).”
BackgroundLoss of Modifier of Cell Adhesion Reveals a Pathway Leading to Axonal Degeneration
Chen, Q., Peto, C. A., Shelton, G. D., Mizisin, A. P., Sawchenko, P. E., & Schubert, D. A. (2009) · Journal of Neuroscience · doi:10.1523/jneurosci.3985-08.2009 · Cited by 65 · cited 2× · see citing works
“In contrast, no functional role can be assigned to Pro1733, suggesting that the p.Pro1733Ala exchange (rs150569245, detected with a frequency of 1.163% in gnomAD) does not critically affect DOCK4 function.”
BackgroundInfluentialMutations in DOCK7 in Individuals with Epileptic Encephalopathy and Cortical Blindness
Perrault, I., Hamdan, F. F., Rio, M., Capo-Chichi, J.-M., Boddaert, N., Décarie, J.-C., Maranda, B., Nabbout, R., Sylvain, M., Lortie, A., et al. (2014) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2014.04.012 · Cited by 50 · cited 1× · see citing works
“…(MIM: #614,219) and DOCK7 (MIM: #615,859), members of the dedicator of cytokinesis (DOCK) family, are Extended author information available on the last page of the article a cause for the Adams–Oliver syndrome (Sukalo et al. 2015) and epileptic encephalopathy (Perrault et al. 2014), respectively.”
BackgroundSukalo, M., Tilsen, F., Kayserili, H., Müller, D., Tüysüz, B., Ruddy, D. M., Wakeling, E., Ørstavik, K. H., Snape, K. M., Trembath, R., et al. (2015) · Human Mutation · doi:10.1002/humu.22795 · Cited by 50 · cited 1× · see citing works
“…(MIM: #614,219) and DOCK7 (MIM: #615,859), members of the dedicator of cytokinesis (DOCK) family, are Extended author information available on the last page of the article a cause for the Adams–Oliver syndrome (Sukalo et al. 2015) and epileptic encephalopathy (Perrault et al. 2014), respectively.”
BackgroundRac GEF Dock4 interacts with cortactin to regulate dendritic spine formation.
Ueda, S., Negishi, M., & Katoh, H. (2013) · Molecular Biology of the Cell · doi:10.1091/mbc.e12-11-0782 · Cited by 47 · cited 2× · see citing works
“The DOCK4 -dependent RAC1 activation has been reported as important for neurite differentiation (Xiao et al. 2013) and interaction with the proline-rich C terminus with cortactin for dendritic spine formation (Ueda et al. 2013).”
BackgroundLeitão, E., Schröder, C., Parenti, I., Dalle, C., Rastetter, A., Kühnel, T., Kuechler, A., Kaya, S., Gérard, B., Schaefer, E., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-34264-y · Cited by 47 · cited 1× · see citing works
“Although the rate of discovery of new rare disease–gene associations has declined in recent years (Ehrhart et al. 2021), several disease-causing genes remain undiscovered, as demonstrated by a recent analysis of the X chromosome (Leitão et al. 2022).”
BackgroundSingle-cell, whole-embryo phenotyping of mammalian developmental disorders
Huang, X., Henck, J., Qiu, C., Sreenivasan, V. K. A., Balachandran, S., Amarie, O. V., de Angelis, M. H., Behncke, R. Y., Chan, W.-L., Despang, A., et al. (2023) · Nature · doi:10.1038/s41586-023-06548-w · Cited by 46 · see citing works
Huang, M., Liang, C., Li, S., Zhang, J., Guo, D., Zhao, B., Liu, Y., Peng, Y., Xu, J., Liu, W., et al. (2020) · Frontiers in Cellular Neuroscience · doi:10.3389/fncel.2019.00577 · Cited by 41 · cited 3× · see citing works
“…to the recommendations of ClinGen (Strande et al. 2017), including the experimental evidence of the published cell culture studies (Ueda et al. 1993; Huang et al. 2019), mouse studies (Guo et al. 2021) and the cohort of the present study, would result in supporting evidence of moderate level.”
BackgroundKlau, J., Jamra, R. A., Radtke, M., Oppermann, H., Lemke, J. R., Beblo, S., & Popp, B. (2021) · European Journal of Human Genetics · doi:10.1038/s41431-021-00981-z · Cited by 36 · see citing works
Self-citationCarnosine inhibits glioblastoma growth independent from PI3K/Akt/mTOR signaling
Oppermann, H., Faust, H., Yamanishi, U., Meixensberger, J., & Gaunitz, F. (2019) · PLoS ONE · doi:10.1371/journal.pone.0218972 · Cited by 35 · cited 1× · see citing works
“Western blotting was performed as described previously (Oppermann et al. 2019).”
MethodSelf-citationA resource to explore the discovery of rare diseases and their causative genes
Ehrhart, F., Willighagen, E., Kutmon, M., et al. (2021) · Scientific Data · doi:10.1038/s41597-021-00905-y · Cited by 30 · cited 1× · see citing works
“Although the rate of discovery of new rare disease–gene associations has declined in recent years (Ehrhart et al. 2021), several disease-causing genes remain undiscovered, as demonstrated by a recent analysis of the X chromosome (Leitão et al. 2022).”
BackgroundCryo-EM structure of the human ELMO1-DOCK5-Rac1 complex
Kukimoto‐Niino, M., Katsura, K., Kaushik, R., Ehara, H., Yokoyama, T., Uchikubo‐Kamo, T., Nakagawa, R., Mishima-Tsumagari, C., Yonemochi, M., Ikeda, M., et al. (2021) · Science Advances · doi:10.1126/sciadv.abg3147 · Cited by 27 · cited 1× · see citing works
“The binding sites of ELMO and RAC1 were deduced from the ELMO1-DOCK5-Rac1 complex (PDB: 7DPA (Kukimoto-Niino et al. 2021)).”
BackgroundDe novo variants in ATP2B1 lead to neurodevelopmental delay
Rahimi, M. J., Urban, N. D., Wegler, M., Sticht, H., Schaefer, M., Popp, B., Gaunitz, F., Morleo, M., Nigro, V., Maitz, S. B., et al. (2022) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2022.03.009 · Cited by 25 · cited 2× · see citing works
“Expression plasmids were generated as described previously (Rahimi et al. 2022), by using full-length human DOCK4 open reading frame (ORF; GeneBank: BC117689; MHS6278-211,690,438) that was obtained from Horizon Discovery BioSciences (Cambridge, UK).”
BackgroundMethodSelf-citation<i><scp>KCNT2</scp>‐</i>Related Disorders: Phenotypes, Functional, and Pharmacological Properties
Cioclu, M. C., Mosca, I., Ambrosino, P., Puzo, D., Bayat, A., Wortmann, S. B., Koch, J., Strehlow, V., Shirai, K., Matsumoto, N., et al. (2023) · Annals of Neurology · doi:10.1002/ana.26662 · Cited by 23 · cited 1× · see citing works
“Nevertheless, this approach is still being used successfully in recent studies to validate the impact of missense variants associated with human disorders (Cioclu et al. 2023).”
BackgroundOppermann, H., Marcos-Grañeda, E., Weiss, L. A., Gurnett, C. A., Jelsig, A. M., Vineke, S. H., Isidor, B., Mercier, S., Magnussen, K., Zacher, P., et al. (2023) · European Journal of Human Genetics · doi:10.1038/s41431-023-01445-2 · Cited by 18 · cited 1× · see citing works
“We have chosen bi-allelic Dock4 KO cells, as relevant effects could be concealed by the analysis of differentiated cells, compared to effects that take place mostly during early development, as demonstrated in heterozygous Cux +/− mice (Oppermann et al. 2023).”
Self-citationVariants in DOCK3 cause developmental delay and hypotonia
Wiltrout, K., Ferrer, A., van de Laar, I., Namekata, K., Harada, T., Klee, E. W., Zimmerman, M. T., Cousin, M. A., Kempainen, J. L., Babovic-Vuksanovic, D., et al. (2019) · European Journal of Human Genetics · doi:10.1038/s41431-019-0397-2 · Cited by 17 · see citing works
Ueda, J.-I., Ozawa, T., Miyazaki, M., et al. (1993) · Inorganica Chimica Acta · doi:10.1016/s0020-1693(00)87522-2 · Cited by 13 · cited 1× · see citing works
“…DOCK4 according to the recommendations of ClinGen (Strande et al. 2017), including the experimental evidence of the published cell culture studies (Ueda et al. 1993; Huang et al. 2019), mouse studies (Guo et al. 2021) and the cohort of the present study, would result in supporting evidence of…”
MethodCRISPR/Cas-Based Approaches to Study Schizophrenia and Other Neurodevelopmental Disorders
Kurishev, A. O., Karpov, D. S., Nadolinskaia, N. I., Гончаренко, А. В., & Голимбет, В. Е. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms24010241 · Cited by 13 · cited 1× · see citing works
“However, novel approaches such as CRISPR/Cas-based methods, the use of human-induced pluripotent stem cells and single-cell analysis will overcome these limitations in the future (Kurishev et al. 2022; Huang et al. 2023).”
BackgroundLarsen, R. (2016) · Springer eBooks · doi:10.1007/978-3-662-50444-4_2 · Cited by 2 · see citing works
Anästhesie und Intensivmedizin für die Fachpflege
Larsen, R. (2016) · doi:10.1007/978-3-662-50444-4
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Yang, Z., Teaney, N. A., Buttermore, E. D., Şahin, M., & Saber, W. A. (2025) · Frontiers in Neuroscience · doi:10.3389/fnins.2024.1524577 · Cited by 4 · see citing works
Bresack, B., Kohl, L. R., Afenjar, A., et al. (2025) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2025.10.015 · Cited by 2 · see citing works
Self-citationEncephalopathy-linked UFM1 variants impede neuronal protein translation, development, and function
Perdigão, C., Torres, J., Magnussen, H., Koch, J., Rudashevskaya, E. L., Moschref, F., Fiošins, M., Benseler, F., Wenger, S., Nilsson, T., et al. (2026) · EMBO Molecular Medicine · doi:10.1038/s44321-026-00389-6 · Cited by 1 · see citing works
“S17C), whose deletion is associated with neurodevelopmental delay and microcephaly, i.e., phenotypes that are also observed in patients with mutations linked to impaired UFMylation (Herbst et al, 2024).”
Choi, N. Y., Ham, S., Jeong, D., et al. (2026) · Journal of Advanced Research · doi:10.1016/j.jare.2026.01.023
Werren, E. A., Vats, P., Rech, G. E., Peracchio, M., King, C., Charnysh, E., Gorham, R. D., Audano, P. A., Robinson, P. N., Kelly, M. A., et al. (2026) · Human Genetics and Genomics Advances · doi:10.1016/j.xhgg.2026.100620
“27 Although the disorder shows phenotypic overlap with each sibling’s clinical features (Table S1; see the supplemental note), c.2498T>A (GenBank: NM_014705.”
Self-citationYan, H., Lv, J., Bai, J., et al. (2026) · Frontiers in Cardiovascular Medicine · doi:10.3389/fcvm.2026.1954425
“The receptor-guided transcytosis pathway, from luminal capture through DOCK4 and RAC1-dependent scission to abluminal release (29, 32, 33), is shown in Figure 3.”
Chrzanowska, J., Karpiński, P., Szczygieł, M., et al. (2026) · Research Square · doi:10.21203/rs.3.rs-10974535/v1
- Authors
- Herbst, C., Bothe, V., Wegler, M., Axer-Schaefer, S., Audebert-Bellanger, S., Gecz, J., Cogne, B., Feldman, H. B., Horn, A. H. C., Hurst, A. C. E., Kelly, M. A., Kruer, M. C., Kurolap, A., Laquerriere, A., Li, M., Mark, P. R., Morawski, M., Nizon, M., Pastinen, T., Polster, T., Saugier-Veber, P., SeSong, J., Sticht, H., Stieler, J. T., Thifffault, I., van Eyk, C. L., Marcorelles, P., Vezain-Mouchard, M., Abou Jamra, R., & Oppermann, H.
- Affiliations
- University Hospital Leipzig (DE)
- Bielefeld University (DE)
- Tel Aviv University (IL)
- Friedrich-Alexander-Universität Erlangen-Nürnberg (DE)
- University of Alabama at Birmingham (US)
- HudsonAlpha Institute for Biotechnology (US)
- Barrow Neurological Institute (US)
- Tel Aviv Sourasky Medical Center (IL)
- Invitae (United States) (US)
- Helen DeVos Children's Hospital (US)
- Leipzig University (DE)
- Centre National de la Recherche Scientifique (FR)
- Children's Mercy Hospital (US)
- Seoul National University (KR)
- Centre Hospitalier Régional Universitaire de Brest (FR)
- Corresponding author
- Oppermann, Henry
- ORCID
- Venue
- Human Genetics
- Published
- 2024-03
- Volume
- 143
- Issue
- 3
- Pages
- 455-469
- ISSN
- 0018-7348 (ISSN-L)
- 0340-6717
- 1432-1203
- PMC
- PMC11043173
- OpenAlex
- W4393161576
- Semantic Scholar
- bfb77b2b74e7509b19afacf88efdcad1c9f93fa2
- Cited by
- 7
- References
- 48
- Citations by year
- 2026: 5 · 2025: 2
- FWCI
- 1.70
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Human Genetics (publishedVersion, cc-by)
- Research Square (acceptedVersion, cc-by)
- PubMed (publishedVersion)
- HAL (Le Centre pour la Communication Scientifique Directe) (submittedVersion, cc-by)
- PUBLISSO (German National Library of Medicine) (submittedVersion, cc-by)
- PubMed Central (submittedVersion, cc-by)
- Adelaide Research & Scholarship (AR&S) (University of Adelaide) (submittedVersion, cc-by)
- Funders
- Universität Leipzig
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Health Sciences › Medicine › Pediatrics, Perinatology and Child Health › Fetal and Pediatric Neurological Disorders
- Keywords
- DOCK4, neurodevelopmental delay, microcephaly, loss-of-function mutations, missense mutations, de novo mutations, maternally inherited variant, Rac1, neurite outgrowth, cytoskeleton, neurodevelopmental disorders, seizures, hypotonia, brain malformations
- MeSH terms
- Loss of Function Mutation, Adolescent, Animals, Child, Developmental Disabilities, Child, Preschool, Female, Heterozygote, Humans, Infant, Male, Microcephaly, Phenotype, Mutation, Missense, GTPase-Activating Proteins, Mice, Neurodevelopmental Disorders
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-14.
Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-14.
Cited sources are checked by gpt-6-sol.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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