A SWI/SNF-related autism syndrome caused by de novo mutations in ADNP
Open accessAbstract
Despite the high heritability of autism spectrum disorders (ASD), characterized by persistent deficits in social communication and interaction and restricted, repetitive patterns of behavior, interests or activities, a genetic diagnosis can be established in only a minority of patients. Known genetic causes include chromosomal aberrations, such as the duplication of the 15q11-13 region, and monogenic causes, as in Rett and fragile-X syndromes. The genetic heterogeneity within ASD is striking, with even the most frequent causes responsible for only 1% of cases at the most. Even with the recent developments in next-generation sequencing, for the large majority of cases no molecular diagnosis can be established. Here, we report ten patients with ASD and other shared clinical characteristics, including intellectual disability and facial dysmorphisms caused by a mutation in ADNP, a transcription factor involved in the SWI/SNF remodeling complex. We estimate this gene to be mutated in at least 0.17% of ASD cases, making it one of the most frequent ASD-associated genes known to date.
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- Findingown data
Targeted screening of ADNP by molecular inversion probes or high-resolution melting in 2,891 patients with syndromic autism spectrum disorder identified four more mutation carriers.
“Next, we targeted ADNP using molecular inversion probes (MIPs) or high resolution melt curve analysis (HRM) in a cohort of 2,891 patients with syndromic ASD and identified four more patients with mutations in this gene.”
Quote in the paperSubstantial claim - Findingown data
Mfold analysis showed that the clustered 4-bp deletions in patients 1, 6 and 8 lie in the stem of the same short hairpin.
“Mfold analysis (web server for nucleic acid folding and hybridization prediction)27 showed that the clustered 4bp deletions of patients 1, 6 and 8 are located in the stem of the same short hairpin (Supplementary Fig. 2).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [27] Zuker, M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31, 3406–3415 (2003). source
Not checked in the free run.
- Findingown data
The authors estimate that ADNP is mutated in at least 0.17% of autism spectrum disorder cases.
“We estimate this gene to be mutated in at least 0.17% of ASD cases”
- Also stated in: § Abstract · hedged
“Mutations in ADNP may explain the etiology of 0.17% of patients with ASD (95% binomial confidence interval: 0.083% - 0.32%)”
Quote in the paperSubstantial claim- Rests on an assumption: The cohort of 5,776 patients screened is representative of the broader autism spectrum disorder population, so the observed ADNP mutation frequency can be used to estimate the proportion of autism spectrum disorder cases explained by ADNP.
- Also stated in: § Abstract · hedged
- Findingown data
A wildtype-specific ADNP assay showed no difference from controls in patients 1, 6 and 8, indicating that the excess ADNP mRNA came from the mutant allele.
“The expression of this ADNPwt amplicon was not different from controls, demonstrating that the excess ADNP mRNA in patients corresponds to the mRNA transcribed from the mutant allele.”
Quote in the paperSubstantial claim - Findingown data
The identified ADNP mutations cluster at specific positions.
“Strikingly, the identified mutations appear to cluster at specific positions.”
Quote in the paperSubstantial claim
- Findingown data
Truncating mutations in ADNP are rare in the general population.
“Putative truncating mutations for ADNP are in fact rare.”
Quote in the paperSubstantial claim - Findingown data
The ADNP mutations were detected in cDNA from lymphoblastoid cell lines of patients 1, 2, 6 and 8.
“Indeed, the mutations were present in the cDNA generated from lymphoblastoid cell lines of patients 1, 2, 6 and 8.”
Quote in the paperSubstantial claim - Findingown data
Additional neuropsychiatric features, including attention deficit/hyperactivity disorder, anxiety disorder and obsessive compulsive behavior, were relatively common in the patients.
“Additional neuropsychiatric features are relatively common, including attention deficit/hyperactivity disorder, anxiety disorder and obsessive compulsive behavior.”
Quote in the paperNot a substantial claim - Findingown data
The authors identified three additional ADNP mutations in 240 patients from three independent whole-exome sequencing studies.
“We subsequently identified three mutations in ADNP in 240 patients from three independent WES studies (Table 1).”
Quote in the paperSubstantial claim - Findingown data
All identified ADNP mutations result in loss of at least the last 166 C-terminal amino acids.
“All mutations result in the loss of at least the 166 last C-terminal amino acids.”
Quote in the paperSubstantial claim - Findingown data
Autism and comorbid mild to severe intellectual disability were consistent features in all ten patients.
“Autism and comorbidity with mild to severe intellectual disability is a consistent feature in all patients (Table 2, Supplementary Note).”
Quote in the paperSubstantial claim - Findingown data
The 4-bp deletion shared by patients 6 and 8 is separated by only one nucleotide from the 4-bp deletion in patient 1.
“This mutation is separated by only one nucleotide from the 4bp deletion in patient 1.”
Quote in the paperSubstantial claim - Findingown data
The 4-bp de novo deletions in patients 6 and 8 are identical despite the patients being unrelated and living in different countries.
“The 4bp de novo deletions in both patient 6 and 8 are identical even though these patients are unrelated and were born and live in different countries.”
Quote in the paperSubstantial claim - Findingown data
The mutations in patients 5 and 10 fall within the 13-bp deletion in patient 4.
“Additonally, the mutations observed in patients 5 and 10 fall within the 13bp deletion in patient 4.”
Quote in the paperSubstantial claim - Findingown data
The authors found no evidence for simple or tandem repeats in the mutation region.
“We found no evidence for the presence of simple or tandem repeats in this region.”
Quote in the paperSubstantial claim - Findingown data
In an initial cohort of ten patients with intellectual disability, autism spectrum disorder and facial dysmorphisms, one patient was found by whole-exome sequencing to have a de novo mutation in ADNP.
“In an initial cohort of 10 patients with intellectual disability, ASD and facial dysmorphisms, we identified a patient with a de novo mutation in the transcription factor ADNP using WES (Supplementary Fig. 1).”
Quote in the paperSubstantial claim - Findingcitation
Almost the entire 1.6 Kb sequence spanned by the mutations is conserved in mammals (PhyloP M=1.52, s=1.25).
“Almost the complete 1.6Kb sequence spanned by the mutations is conserved in mammals (PhyloP M=1.52, s=1.25)26.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [26] Pollard, K.S., Hubisz, M.J., Rosenbloom, K.R. & Siepel, A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 20, 110–121 (2010). source
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- Findingown data
The authors found no additional non-synonymous de novo variants in the patients.
“We found no additional non-synonymous de novo variants.”
Quote in the paperSubstantial claim - Findingown data
The frequency of truncating ADNP mutations was significantly higher in the patient cohort than in ESP and Simons Siblings controls (p = 0.001852, odds ratio 13.24668, one-sided Fisher's exact test).
“The frequency of truncating mutations in ADNP is significantly higher (p: 0.001852, odds ratio 13.24668, one-sided Fisher’s exact test) in patients compared to the ESP and Simons Siblings controls.”
Quote in the paperSubstantial claim- Rests on an assumption: The control cohorts used for comparison are representative of the general population and comparable to the patient cohort for the ADNP truncating-mutation frequency analysis.
- Findingown data
Using a probabilistic model based on human-chimpanzee fixed differences and sequence context, and assuming a de novo rate of 1.2 non-synonymous coding variants per individual, the probability of detecting eight or more de novo truncating ADNP events in the cohort was p = 2.65e-18 by binomial test.
“Under a de novo rate of 1.2 non-synonymous coding variants per individual, we estimate the probability of detecting eight or more de novo truncating events in ADNP within our cohort as p = 2.65e-18 (binomial test).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [16] O'Roak, B.J. et al. Multiplex targeted sequencing identifies recurrently mutated genes in autism spectrum disorders. Science 338, 1619–1622 (2012). source
Not checked in the free run.
- Findingown data
Among genes reported as differentially expressed in Adnp-/- and Adnp+/- mice, only PLAGL2 was differentially regulated in the patients.
“Of the other genes reported as differentially expressed in Adnp-/-23 and Adnp+/-18 mice (down: CCNC, TMPO, PLAGL2; up: ABCF3), only PLAGL2 was found to be differentially regulated in our patients (Supplementary Fig. 3e).”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [23] Mandel, S., Rechavi, G. & Gozes, I. Activity-dependent neuroprotective protein (ADNP) differentially interacts with chromatin to regulate genes essential for embryogenesis. Dev. Biol. 303, 814–824 (2007). source
Not checked in the free run.
- cites [18] Vulih-Shultzman, I. et al. Activity-dependent neuroprotective protein snippet NAP reduces tau hyperphosphorylation and enhances learning in a novel transgenic mouse model. J. Pharmacol. Exp. Ther. 323, 438–449 (2007). source
Not checked in the free run.
- Findingown data
Across the study, ten ADNP mutations were found among 5,776 patients.
“In total, ten mutations were found in 5,776 patients.”
Quote in the paperSubstantial claim - Findingown data
Total ADNP mRNA levels were significantly increased by 41% in patients 1, 2, 6 and 8.
“The total level of ADNP mRNA was significantly increased by 41% in patients 1, 2, 6 and 8 (Supplementary Fig. 3b, Table 3).”
Quote in the paperSubstantial claim - Findingown data
The authors found no indication of a correlation between individual ADNP mutations and clinical presentation.
“At the moment, there are no indications for a correlation between the individual mutations and the clinical presentation.”
Quote in the paperNot a substantial claim - Findingown data
In the four deletion cases where parents were tested, the deletion was de novo.
“In the four cases where the parents were tested, the deletion was de novo.”
Quote in the paperSubstantial claim - Findingcitation
In the authors' databases and DECIPHER, five deletions of 313 Kb to 3.31 Mb removing 5 to 23 genes including part or all of ADNP have been described.
“In our own databases and in DECIPHER35, five deletions with sizes 313Kb-3.31Mb, taking away 5-23 genes including (part of) ADNP, have been described.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [35] Firth, H.V. et al. DECIPHER: database of chromosomal imbalance and phenotype in humans using ensembl resources. Am. J. Hum. Genet. 84, 524–533 (2009). source
Not checked in the free run.
- Findingown data
Mutations in ADNP may explain the etiology of 0.17% of patients with autism spectrum disorder (95% binomial confidence interval 0.083% to 0.32%).
“Mutations in ADNP may explain the etiology of 0.17% of patients with ASD (95% binomial confidence interval: 0.083% - 0.32%)”
Quote in the paperSubstantial claim- Rests on an assumption: The cohort of 5,776 patients screened is representative of the broader autism spectrum disorder population, so the observed ADNP mutation frequency can be used to estimate the proportion of autism spectrum disorder cases explained by ADNP.
- Findingown data
Patients with ADNP deletions share some clinical characteristics with the patients reported here who carry truncating mutations.
“The patients with ADNP deletions all share some clinical characteristics with the patients reported here, carrying truncating mutations (Supplementary Fig. 4, Supplementary Table 1).”
Quote in the paperNot a substantial claim - Findingown data
These three patients did not share more clinical characteristics with each other than with other patients.
“Yet, these three patients do not share more clinical characteristics amongst each other than with other patients.”
Quote in the paperNot a substantial claim - Premisecitation
A role for ADNP in neuronal cell differentiation and maturation was suggested by a study observing decreased embryoid body number and size and fewer neurites after ADNP knockdown with shRNA in P19 cells.
“A role in neuronal cell differentiation and maturation was suggested after observing a substantial decrease in the number and size of embryoid bodies and the number of neurites after knockdown of ADNP with shRNA in P19 cells17.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [17] Mandel, S., Spivak-Pohis, I. & Gozes, I. ADNP differential nucleus/cytoplasm localization in neurons suggests multiple roles in neuronal differentiation and maintenance. J. Mol. Neurosci. 35, 127–141 (2008). source
Not checked in the free run.
- Premisecitation
Adnp-/- mice are not viable because of failure of neural tube closure.
“Furthermore, Adnp-/- mice are not viable due to failure of the neural tube closure”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [34] Pinhasov, A. et al. Activity-dependent neuroprotective protein: a novel gene essential for brain formation. Brain Res. Dev. Brain Res. 144, 83–90 (2003). source
Not checked in the free run.
- Interpretationown data
Mutations in ADNP cause a recurrent SWI/SNF-related autism syndrome.
“caused by a mutation in ADNP”
- Also stated in: § Abstract · plain
“In summary, we identified a recurrent SWI/SNF-related ASD syndrome, caused by mutations in ADNP.”
Quote in the paperSubstantial claim - Also stated in: § Abstract · plain
- Interpretationown data
ADNP is one of the most frequent autism spectrum disorder genes known to date.
“making it one of the most frequent ASD genes known to date”
- Also stated in: § Abstract · plain
“thus constitute one of the most frequent known causes of autism.”
Quote in the paperSubstantial claim - Also stated in: § Abstract · plain
- Interpretationreasoning
The authors suggest that deregulation of this negative feedback leads to increased ADNP mRNA in an attempt to restore homeostasis.
“This suggests a deregulation of the negative feedback leading to increased levels of ADNP mRNA in order to restore homeostasis.”
Quote in the paperSubstantial claim - Interpretationcitation
Because no exon-exon boundary in ADNP mRNA lies downstream of any of the mutations, nonsense-mediated RNA decay is unlikely.
“Since no exon-exon boundary in the ADNP mRNA is present downstream from any of the mutations, nonsense mediated RNA decay (NMD) is unlikely28-30.”
Quote in the paperSubstantial claim0 of 3 sources checked- cites [28] Nagy, E. & Maquat, L.E. A rule for termination-codon position within intron-containing genes: when nonsense affects RNA abundance. Trends Biochem. Sci. 23, 198–199 (1998). source
Not checked in the free run.
- cites [29] Schoenberg, D.R. & Maquat, L.E. Regulation of cytoplasmic mRNA decay. Nat. Rev. Genet. 13, 246–259 (2012). source
Not checked in the free run.
- cites [30] Kervestin, S. & Jacobson, A. NMD: a multifaceted response to premature translational termination. Nat. Rev. Mol. Cell Biol. 13, 700–712 (2012). source
Not checked in the free run.
- Interpretationown data
The authors suggest that the underlying mutational mechanism may involve a DNA repair defect after replication fork pausing at these hairpins.
“Hence, we suggest that the underlying mechanism of the mutations may involve a DNA repair defect following pausing of a replication fork at these hairpins.”
Quote in the paperSubstantial claim - Interpretationcitation
ADNP has multiple cellular functions that appear compatible with the clinical presentation of the patients.
“ADNP has multiple cellular functions that seem compatible with the clinical presentation of our patients.”
Quote in the paperSubstantial claim - Premisenone given
No patients with a pure deletion of ADNP have been reported.
“No patients with a pure deletion of ADNP have been reported.”
Quote in the paperNot a substantial claim - Premisecitation
The C-terminal part of ADNP directly interacts with ARID1A, SMARCA4 and SMARCC2, three essential components of the BAF complexes.
“The C-terminal part of ADNP directly interacts with ARID1A, SMARCA4 and SMARCC2, three essential components of the BAF complexes, the functional eukaryotic equivalent of the SWI/SNF complex in yeast that is involved in the regulation of gene expression36.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [36] Mandel, S. & Gozes, I. Activity-dependent neuroprotective protein constitutes a novel element in the SWI/SNF chromatin remodeling complex. J. Biol. Chem. 282, 34448–34456 (2007). source
Not checked in the free run.
- Study design and conductown data
Firm conclusions about a possible genotype-phenotype correlation cannot be drawn because of the small sample size.
“However, at this moment it is not possible to draw firm conclusions on a possible genotype:phenotype correlation due to the small sample size.”
Quote in the paperSubstantial claim - Interpretationreasoning
The findings will increase the diagnostic yield in the autism spectrum disorder population.
“Our findings will increase the diagnostic yield in this population”
Quote in the paperSubstantial claim - Interpretationown data
ADNP mutations constitute one of the most frequent known causes of autism.
“and thus constitute one of the most frequent known causes of autism.”
Quote in the paperSubstantial claim
- Classified as probably not a substantial claim. 18
- May combine two claims. 24
- The quote only partly states this claim. 1
Probably not a substantial claim: may not pass S3 (load-bearing).
Findingown dataA seizure disorder was observed in two patients.
“A seizure disorder was noted in two patients.”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataNone of the ten ADNP mutations were found in the 1,000 Genomes Project, in 1,728 unaffected siblings from the Simons Simplex Collection screened by molecular inversion probes, or in 192 healthy Belgian control chromosomes analyzed by high-resolution melting.
“None were present in the 1,000 Genomes Project19, in 1,728 MIP sequenced unaffected siblings form the Simons Simplex Collection, or in 192 HRM analyzed chromosomes from healthy Belgian controls.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [19] Abecasis, G.R. et al. An integrated map of genetic variation from 1,092 human genomes. Nature 491, 56–65 (2012). source
Not checked in the free run.
The quote only partly states this claim.
Findingown dataTP53 expression was significantly increased in the patients.
“Expression levels of TP53, reported upregulated in HT29 cells incubated with ADNP antioligodeoxynucleotide32, were significantly increased (Supplementary Fig. 3g)”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [32] Zamostiano, R. et al. Cloning and characterization of the human activity-dependent neuroprotective protein. J. Biol. Chem. 276, 708–714 (2001). source
Not checked in the free run.
May combine two claims.
Findingown dataThe patients' dysmorphic features included a prominent forehead, high hairline, eversion or notch of the eyelid, broad nasal bridge, thin upper lip and smooth or long philtrum.
“Dysmorphic features include a prominent forehead, high hairline, eversion or notch of the eyelid, broad nasal bridge, thin upper lip and smooth/long philtrum (Figure 1).”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataAll identified ADNP mutations were heterozygous frameshift or nonsense variants located in the C-terminal part of the last exon and introduced a premature termination codon.
“All mutations are heterozygous frameshift or nonsense variants in the C-terminal part of the last exon of ADNP and result in a premature termination codon (Table 1).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataThe authors found no X-chromosomal, compound heterozygous or homozygous variants in known intellectual disability or autism spectrum disorder genes.
“Neither did we find X-chromosomal, compound or homozygous variants in known intellectual disability/ASD genes.”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataThe authors identified ten patients with autism spectrum disorder and additional shared clinical features, including intellectual disability and facial dysmorphisms, who carry mutations in ADNP.
“Here, we report 10 patients with ASD and other shared clinical characteristics, including intellectual disability and facial dysmorphisms caused by a mutation in ADNP, a transcription factor involved in the SWI/SNF remodeling complex.”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataThe patients frequently had hypotonia, feeding problems in infancy and congenital heart defects.
“Other frequent findings include hypotonia, feeding problems in infancy and congenital heart defects.”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataFor nine of the ten patients, parental testing was available and the ADNP mutation appeared de novo in every case.
“For nine patients the parents were available for testing and in each case the mutation appeared de novo (Table 1).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataDysmorphic features varied between patients, but a prominent forehead, broad nasal bridge, thin upper lip and smooth philtrum were frequently present.
“Dysmorphic features vary from patient to patient, but a prominent forehead, broad nasal bridge, thin upper lip and smooth philtrum are frequently present.”
Quote in the paperNot a substantial claimMay combine two claims.
Findingnone givenThe mutations in patients 6 and 8 are identical and differ by only one amino acid from the mutation in patient 1.
“The mutations in patients 6 and 8 are identical and differ only by a single amino acid from the mutation in patient 1.”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataThe severity of the phenotype varied in the cohort, but all patients had some degree of autism spectrum disorder and all were intellectually disabled.
“The severity of the phenotype in our cohort varies, but all patients exhibit various degrees of ASD and all are intellectually disabled.”
Quote in the paperSubstantial claimMay combine two claims.
PremisecitationADNP is a transcription factor that participates in the SWI/SNF chromatin remodeling complex.
“a transcription factor involved in the SWI/SNF remodeling complex”
- Also stated in: § Abstract · plain
“The C-terminal part of ADNP directly interacts with ARID1A, SMARCA4 and SMARCC2, three essential components of the BAF complexes, the functional eukaryotic equivalent of the SWI/SNF complex in yeast that is involved in the regulation of gene expression36.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [36] Mandel, S. & Gozes, I. Activity-dependent neuroprotective protein constitutes a novel element in the SWI/SNF chromatin remodeling complex. J. Biol. Chem. 282, 34448–34456 (2007). source
Not checked in the free run.
- Also stated in: § Abstract · plain
May combine two claims.
PremisecitationDe novo loss-of-function mutations in ADNP had previously been reported in two autism spectrum disorder patients by whole-exome sequencing and targeted resequencing, but those studies did not establish locus-specific significance for causality.
“De novo loss of function mutations in this gene had previously been identified in two patients by WES2 and targeted resequencing16 of patients with ASD. In those studies however, causal relationship did not reach locus-specific significance.”
Quote in the paperSubstantial claim0 of 2 sources checked- cites [2] O'Roak, B.J. et al. Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature 485, 246–250 (2012). source
Not checked in the free run.
- cites [16] O'Roak, B.J. et al. Multiplex targeted sequencing identifies recurrently mutated genes in autism spectrum disorders. Science 338, 1619–1622 (2012). source
Not checked in the free run.
May combine two claims.
InterpretationcitationBecause ADNP expression is controlled by an autoregulatory negative feedback loop, the overall upregulation might result from the mutant protein's inability to bind the ADNP promoter.
“Since ADNP expression is under control of an autoregulatory negative feedback loop33, the overall upregulation might be a consequence of the inability of the mutant protein to bind the ADNP promoter.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [33] Aboonq, M.S., Vasiliou, S.A., Haddley, K., Quinn, J.P. & Bubb, V.J. Activity-dependent neuroprotective protein modulates its own gene expression. J. Mol. Neurosci. 46, 33–39 (2012). source
Not checked in the free run.
May combine two claims.
Interpretationown dataThe clustering of de novo rare variants suggests a mutation predisposition mechanism, possibly due to local genomic architecture.
“Clustering of de novo, rare variants is suggestive of a mutation predisposition mechanism, potentially as a result of a particular local genomic architecure.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
InterpretationreasoningThe discrepancy for the other mouse genes may be due to differences in tissue and developmental stage between knockout mice and human cell lines.
“This may be the consequence of differences in tissue and developmental stage between the knockout mice and the human cell lines.”
Quote in the paperNot a substantial claimMay combine two claims.
PremisecitationAn inherited p.Gly1094Profs*5 ADNP mutation identified by molecular inversion probe sequencing is located nine amino acids from the C-terminal end and is not associated with any protein domains.
“An inherited p.Gly1094Profs*5 mutation was identified by MIP sequencing16 but the reported frameshift is the ninth amino acid from the C-terminal end of the protein and not associated with any protein domains.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [16] O'Roak, B.J. et al. Multiplex targeted sequencing identifies recurrently mutated genes in autism spectrum disorders. Science 338, 1619–1622 (2012). source
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing).
InterpretationreasoningThe increase in TP53 may result from augmented cellular stress due to overall deregulation of genes under ADNP transcriptional control.
“possibly as a result of augmented cellular stress due to an overall deregulation of genes under transcriptional control of ADNP.”
Quote in the paperNot a substantial claimMay combine two claims.
PremisecitationADNP+/- mice show tauopathy, neuronal cell death and abnormalities in social behaviour and cognitive functioning.
“while ADNP+/- mice show tauopathy, neuronal cell death and abnormalities in social behaviour and cognitive functioning18,34.”
Quote in the paperSubstantial claim0 of 2 sources checked- cites [18] Vulih-Shultzman, I. et al. Activity-dependent neuroprotective protein snippet NAP reduces tau hyperphosphorylation and enhances learning in a novel transgenic mouse model. J. Pharmacol. Exp. Ther. 323, 438–449 (2007). source
Not checked in the free run.
- cites [34] Pinhasov, A. et al. Activity-dependent neuroprotective protein: a novel gene essential for brain formation. Brain Res. Dev. Brain Res. 144, 83–90 (2003). source
Not checked in the free run.
May combine two claims.
InterpretationreasoningThe authors' findings expand the phenotypic spectrum of SWI/SNF-related disorders, several of which are caused by mutations in direct interaction partners of ADNP.
“These findings expand the phenotypic spectrum of SWI/SNF-related disorders, several of which are caused by mutations in direct interaction partners of ADNP.”
Quote in the paperSubstantial claimClassified as probably not a substantial claim. May combine two claims.
Study design and conductown dataWhole-exome sequencing variants were filtered to exclude low-quality variants, intronic or intergenic variants except splice sites, and variants inherited from parents.
“Variants were filtered by VariantDB (see URLs, manuscript in preparation) to exclude variants with (1) low quality, using thresholds based on correlation between NGS data and SNP-chip genotyping; (2) intronic or intergenic location, except splice sites; and (3) inheritance from the parents.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductcitationReference genes YWHAZ and HPRT were selected according to geNorm calculations.
“YWHAZ and HPRT were selected as reference genes, according to geNorm calculations54.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [54] Vandesompele, J. et al. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 3, 34.1–34.11 (2002). source
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Probably not a substantial claim: may not pass S1 (asserted). May combine two claims.
InterpretationreasoningThe authors hypothesize that the mutant ADNP protein with an altered C-terminal structure will hamper BAF complex recruitment while still occupying DNA binding sites.
“Hence, it can be hypothesised that the mutant protein with an altered C-terminal structure will hamper the recruitment of the BAF complex, while it still occupies DNA binding sites.”
Quote in the paperNot a substantial claimClassified as probably not a substantial claim.
PremisecitationA switch in BAF complex composition is essential for initiating post-mitotic activity-dependent dendritic outgrowth and axonal development.
“A switch of complex composition is essential for initiation of post-mitotic activity-dependent dendritic outgrowth and axonal development.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [38] Lessard, J. et al. An essential switch in subunit composition of a chromatin remodeling complex during neural development. Neuron 55, 201–215 (2007). source
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductown dataThe amplification efficiency of the qPCR primers was assessed and confirmed to be above 1.85.
“The amplification efficiency of the different primers was assessed and confirmed to be above 1.85.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S1 (asserted). May combine two claims.
Interpretationown dataBecause mutant RNA was detected in the patients, the authors hypothesize that the mutant ADNP protein competes with wildtype protein in aberrant interaction with the BAF complex.
“As we were able to detect mutant RNA in our patients, we hypothesize that the mutant ADNP protein competes with the wildtype protein in aberrant interaction with the BAF complex.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductnone givenClinical evaluation was performed by at least one expert clinical geneticist.
“Clinical evaluation was performed by at least one expert clinical geneticist.”
Quote in the paperNot a substantial claimMay combine two claims.
Premisenone givenWildtype ADNP directly binds target genomic regions and mediates recruitment of the BAF complex through its C-terminal end.
“Wildtype ADNP directly binds target genomic regions and mediates the recruitment of the BAF complex through the C-terminal end.”
Quote in the paperNot a substantial claimClassified as probably not a substantial claim.
Study design and conductnone givenInheritance determination and validation for molecular inversion probe-discovered patients were performed by Sanger sequencing.
“Inheritance determination and validation were performed by Sanger sequencing.”
Quote in the paperSubstantial claimClassified as probably not a substantial claim.
Study design and conductnone givenReported de novo mutations were confirmed by an independent technique such as Sanger sequencing.
“Presence of reported (de novo) mutations were confirmed by an independent technique such as Sanger sequencing.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductnone givenExpression values from two cDNA syntheses from two RNA isolations per patient were compared with values from eight control individuals.
“Expression values of two cDNA syntheses originating from two different RNA isolations per patient were compared to the values obtained from eight control individuals.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationBAF complexes are ATP-dependent chromatin remodeling complexes consisting of 15 subunits, including one of the ATPase core subunits SMARCA4 or SMARCA2.
“These ATP-dependent chromatin remodelling complexes consist of 15 subunits, including one of both ATPase core subunits SMARCA4 or SMARCA237.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [37] Ronan, J.L., Wu, W. & Crabtree, G.R. From neural development to cognition: unexpected roles for chromatin. Nat. Rev. Genet. 14, 347–359 (2013). source
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Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
Study design and conductnone givenWritten informed consent was obtained for all patients, and consent for publication of photographs was obtained for patients 1, 2, 4, 5, 6 and 8.
“Written informed consent for inclusion in the study was obtained for all patients and consent for the publication of photographs was obtained for patients 1, 2, 4, 5, 6 and 8.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationThe phenotype associated with mutations in these BAF component genes ranges from non-syndromic intellectual disability with hypotonia and speech delay to recognizable syndromes such as Coffin-Siris syndrome and Nicolaides-Baraitser syndrome.
“The phenotype associated with mutations in these genes ranges from non-syndromic intellectual disability with hypotonia and speech delay to recognizable syndromes such as the Coffin-Siris syndrome and Nicolaides-Baraitser syndrome.”
Quote in the paperNot a substantial claim0 of 3 sources checked- cites [39] Kosho, T. et al. Clinical correlations of mutations affecting six components of the SWI/SNF complex: detailed description of 21 patients and a review of the literature. Am. J. Med. Genet. 161A, 1221–1237 (2013). source
Not checked in the free run.
- cites [40] Santen, G.W. et al. Coffin-Siris syndrome and the BAF complex: genotype-phenotype study in 63 patients. Hum. Mutat. 34, 1519–1528 (2013). source
Not checked in the free run.
- cites [41] Hoyer, J. et al. Haploinsufficiency of ARID1B, a member of the SWI/SNF-a chromatin-remodeling complex, is a frequent cause of intellectual disability. Am. J. Hum. Genet. 90, 565–572 (2012). source
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationMutations in six BAF complex components (SMARCB1, SMARCA4, SMARCA2, SMARCE1, ARID1A and ARID1B) have been reported in patients with intellectual disability.
“Interestingly, mutations in patients with intellectual disability have been reported in six components of these complexes (SMARCB1, SMARCA4, SMARCA2, SMARCE1, ARID1A and ARID1B).”
Quote in the paperNot a substantial claim0 of 3 sources checked- cites [39] Kosho, T. et al. Clinical correlations of mutations affecting six components of the SWI/SNF complex: detailed description of 21 patients and a review of the literature. Am. J. Med. Genet. 161A, 1221–1237 (2013). source
Not checked in the free run.
- cites [40] Santen, G.W. et al. Coffin-Siris syndrome and the BAF complex: genotype-phenotype study in 63 patients. Hum. Mutat. 34, 1519–1528 (2013). source
Not checked in the free run.
- cites [41] Hoyer, J. et al. Haploinsufficiency of ARID1B, a member of the SWI/SNF-a chromatin-remodeling complex, is a frequent cause of intellectual disability. Am. J. Hum. Genet. 90, 565–572 (2012). source
Not checked in the free run.
Classified as probably not a substantial claim. May combine two claims.
InterpretationreasoningThis impairment will lead to diminished BAF complex functionality and ultimately deregulation of several cellular processes.
“This will lead to a diminished functionality of the complex and ultimately to deregulation of several cellular processes.”
Quote in the paperSubstantial claim
The paper relies on this without support.
The cohort of 5,776 patients screened is representative of the broader autism spectrum disorder population, so the observed ADNP mutation frequency can be used to estimate the proportion of autism spectrum disorder cases explained by ADNP.
“We estimate this gene to be mutated in at least 0.17% of ASD cases”
“Mutations in ADNP may explain the etiology of 0.17% of patients with ASD (95% binomial confidence interval: 0.083% - 0.32%)”
The paper relies on this without support.
The control cohorts used for comparison are representative of the general population and comparable to the patient cohort for the ADNP truncating-mutation frequency analysis.
“The frequency of truncating mutations in ADNP is significantly higher (p: 0.001852, odds ratio 13.24668, one-sided Fisher’s exact test) in patients compared to the ESP and Simons Siblings controls.”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Deep phenotyping of 10 patients with ADNP mutations led to identification of a potential new syndrome.
“Deep phenotyping of 10 patients with ADNP mutations has led to the identification of a potential new syndrome (67).”
From Genetics and genomics of autism spectrum disorder: embracing complexity (2015) · cites this paper as [67]
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- Authors
- Helsmoortel, C., Vulto-van Silfhout, A. T., Coe, B. P., Vandeweyer, G., Rooms, L., van den Ende, J., Schuurs-Hoeijmakers, J. H. M., Marcelis, C. L., Willemsen, M. H., Vissers, L. E. L. M., Yntema, H. G., Bakshi, M., Wilson, M., Witherspoon, K. T., Malmgren, H., Nordgren, A., Annerén, G., Fichera, M., Bosco, P., Romano, C., de Vries, B. B. A., Kleefstra, T., Kooy, R. F., Eichler, E. E., & Van der Aa, N.
- Affiliations
- University of Antwerp (BE)
- Howard Hughes Medical Institute (US)
- Radboud University Medical Center (NL)
- Westmead Hospital (AU)
- Children's Hospital at Westmead (AU)
- Karolinska Institutet (SE)
- Uppsala University (SE)
- University of Catania (IT)
- Oasi Maria SS (IT)
- Radboud University Nijmegen (NL)
- Corresponding author
- Kooy, R Frank
- ORCID
- Venue
- Nature Genetics
- Published
- 2014-02-16
- Volume
- 46
- Issue
- 4
- Pages
- 380-384
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC3990853
- OpenAlex
- W2097496333
- Semantic Scholar
- 64e7e00926d98492f0281d741ea5654bf44f343f
- Cited by
- 354
- References
- 58
- Citations by year
- 2026: 19 · 2025: 31 · 2024: 43 · 2023: 24 · 2022: 28 · 2021: 25 · 2020: 32 · 2019: 30 · 2018: 28 · 2017: 30 · 2016: 28 · 2015: 21 · 2014: 13
- FWCI
- 20.09
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Radboud Repository (Radboud University) (submittedVersion)
- Funders
- National Institute of Mental Health (R01MH101221)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
- Life Sciences › Neuroscience › Cognitive Neuroscience › Autism Spectrum Disorder Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Keywords
- autism spectrum disorder, ADNP, de novo mutations, SWI/SNF complex, intellectual disability, facial dysmorphism, transcription factors, genetic diagnosis, genetic heterogeneity
- MeSH terms
- Abnormalities, Multiple, Base Sequence, Child Development Disorders, Pervasive, Chromosomal Proteins, Non-Histone, Humans, Molecular Sequence Data, Nerve Tissue Proteins, Transcription Factors, Frameshift Mutation, Sequence Analysis, DNA, Codon, Nonsense, Homeodomain Proteins, Gene Components, Exome, Real-Time Polymerase Chain Reaction
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 2026-10-06.
Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-06.
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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