CHD1chromodomain helicase DNA binding protein 1
Autism Reports / Total Reports
11 / 14Rare Variants / Common Variants
21 / 0Aliases
-Associated Syndromes
-Chromosome Band
5q15-q21.1Associated Disorders
ID, ASD, EPSRelevance to Autism
A de novo damaging missense variant and a de novo frameshift variant in the CHD1 gene have been identified in ASD probands from the Autism Sequencing Consortium and the Simons Simplex Collection (Neale et al., 2012; Iossifov et al., 2014). Pilarowski et al., 2017 described six patients with heterozygous CHD1 missense variants; two of these patients were diagnosed with autism.
Molecular Function
The CHD family of proteins is characterized by the presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template.ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. Regulates polymerase II transcription. Also required for efficient transcription by RNA polymerase I, and more specifically the polymerase I transcription termination step. Regulates negatively DNA replication. Not only involved in transcription-related chromatin-remodeling, but also required to maintain a specific chromatin configuration across the genome. Is also associated with histone deacetylase (HDAC) activity
External Links
SFARI Genomic Platforms
Reports related to CHD1 (14 Reports)
# | Type | Title | Author, Year | Autism Report | Associated Disorders |
---|---|---|---|---|---|
1 | Primary | Patterns and rates of exonic de novo mutations in autism spectrum disorders | Neale BM , et al. (2012) | Yes | - |
2 | Support | The contribution of de novo coding mutations to autism spectrum disorder | Iossifov I et al. (2014) | Yes | - |
3 | Support | Recurrent de novo mutations implicate novel genes underlying simplex autism risk | O'Roak BJ , et al. (2014) | Yes | - |
4 | Recent Recommendation | Missense variants in the chromatin remodeler CHD1 are associated with neurodevelopmental disability | Pilarowski GO , et al. (2017) | No | ASD, ID, epilepsy/seizures |
5 | Support | Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism | Satterstrom FK et al. (2020) | Yes | - |
6 | Support | - | Mahjani B et al. (2021) | Yes | - |
7 | Support | - | Li D et al. (2022) | Yes | - |
8 | Support | - | Zhou X et al. (2022) | Yes | - |
9 | Support | - | Li S et al. (2023) | No | - |
10 | Support | - | Hu C et al. (2023) | Yes | - |
11 | Support | - | Sheth F et al. (2023) | Yes | DD, ID |
12 | Support | - | Ana Karen Sandoval-Talamantes et al. (2023) | Yes | - |
13 | Recent Recommendation | - | Kuokuo Li et al. (2024) | Yes | - |
14 | Support | - | Axel Schmidt et al. (2024) | No | ID |
Rare Variants (21)
Status | Allele Change | Residue Change | Variant Type | Inheritance Pattern | Parental Transmission | Family Type | PubMed ID | Author, Year |
---|---|---|---|---|---|---|---|---|
c.2569-11A>G | - | intron_variant | De novo | - | - | 31981491 | Satterstrom FK et al. (2020) | |
c.13_14del | p.Ser5Ter | frameshift_variant | Unknown | - | - | 34968013 | Li D et al. (2022) | |
c.5069C>A | p.Pro1690Gln | missense_variant | De novo | - | - | 35982159 | Zhou X et al. (2022) | |
c.990C>T | p.Asn330%3D | synonymous_variant | De novo | - | - | 35982159 | Zhou X et al. (2022) | |
c.2157T>A | p.Ser719Arg | missense_variant | Unknown | - | - | 34615535 | Mahjani B et al. (2021) | |
c.472T>C | p.Ser158Pro | missense_variant | De novo | - | - | 39039281 | Axel Schmidt et al. (2024) | |
c.5113T>C | p.Ser1705Pro | missense_variant | De novo | - | Simplex | 36625521 | Li S et al. (2023) | |
c.1241A>G | p.Gln414Arg | missense_variant | Unknown | - | - | 39039281 | Axel Schmidt et al. (2024) | |
c.2092G>A | p.Val698Ile | missense_variant | Familial | Paternal | - | 37007974 | Hu C et al. (2023) | |
c.258T>C | p.Phe86%3D | synonymous_variant | De novo | - | Simplex | 35982159 | Zhou X et al. (2022) | |
c.4886C>G | p.Ser1629Cys | missense_variant | Unknown | - | - | 39039281 | Axel Schmidt et al. (2024) | |
c.421A>G | p.Arg141Gly | missense_variant | Unknown | - | - | 28866611 | Pilarowski GO , et al. (2017) | |
c.1379G>A | p.Arg460Lys | missense_variant | De novo | - | - | 28866611 | Pilarowski GO , et al. (2017) | |
c.1853G>A | p.Arg618Gln | missense_variant | De novo | - | - | 28866611 | Pilarowski GO , et al. (2017) | |
c.2570A>G | p.Asp857Gly | missense_variant | De novo | - | - | 28866611 | Pilarowski GO , et al. (2017) | |
c.3046C>G | p.Leu1016Val | missense_variant | De novo | - | Simplex | 22495311 | Neale BM , et al. (2012) | |
c.3608G>A | p.Arg1203Gln | missense_variant | De novo | - | Simplex | 25418537 | O'Roak BJ , et al. (2014) | |
c.4757G>A | p.Arg1586His | missense_variant | Familial | Paternal | Simplex | 37543562 | Sheth F et al. (2023) | |
c.5123G>A | p.Arg1708Gln | missense_variant | Unknown | - | Multiplex | 28866611 | Pilarowski GO , et al. (2017) | |
c.4550dup | p.Leu1517PhefsTer7 | frameshift_variant | De novo | - | Simplex | 25363768 | Iossifov I et al. (2014) | |
c.315G>C | p.Gln105His | missense_variant | Unknown | - | - | 38003033 | Ana Karen Sandoval-Talamantes et al. (2023) |
Common Variants
No common variants reported.
SFARI Gene score
Strong Candidate, Syndromic
A de novo damaging missense variant and a de novo frameshift variant in the CHD1 gene have been identified in ASD probands from the Autism Sequencing Consortium and the Simons Simplex Collection (Neale et al., 2012; Iossifov et al., 2014). Pilarowski et al., 2017 described six patients with heterozygous CHD1 missense variants; two of these patients were diagnosed with autism.
Score Delta: Score remained at 2S
criteria met
See SFARI Gene'scoring criteriaWe considered a rigorous statistical comparison between cases and controls, yielding genome-wide statistical significance, with independent replication, to be the strongest possible evidence for a gene. These criteria were relaxed slightly for category 2.
The syndromic category includes mutations that are associated with a substantial degree of increased risk and consistently linked to additional characteristics not required for an ASD diagnosis. If there is independent evidence implicating a gene in idiopathic ASD, it will be listed as "#S" (e.g., 2S, 3S, etc.). If there is no such independent evidence, the gene will be listed simply as "S."
4/1/2022
Decreased from 3S to 2S
Description
A de novo damaging missense variant and a de novo frameshift variant in the CHD1 gene have been identified in ASD probands from the Autism Sequencing Consortium and the Simons Simplex Collection (Neale et al., 2012; Iossifov et al., 2014). Pilarowski et al., 2017 described six patients with heterozygous CHD1 missense variants; two of these patients were diagnosed with autism.
10/1/2019
Decreased from 4S to 3S
New Scoring Scheme
Description
A de novo damaging missense variant and a de novo frameshift variant in the CHD1 gene have been identified in ASD probands from the Autism Sequencing Consortium and the Simons Simplex Collection (Neale et al., 2012; Iossifov et al., 2014). Pilarowski et al., 2017 described six patients with heterozygous CHD1 missense variants; two of these patients were diagnosed with autism.
Reports Added
[New Scoring Scheme]10/1/2017
Increased from to 4S
Description
A de novo damaging missense variant and a de novo frameshift variant in the CHD1 gene have been identified in ASD probands from the Autism Sequencing Consortium and the Simons Simplex Collection (Neale et al., 2012; Iossifov et al., 2014). Pilarowski et al., 2017 described six patients with heterozygous CHD1 missense variants; two of these patients were diagnosed with autism.
Krishnan Probability Score
Score 0.49468564801236
Ranking 3492/25841 scored genes
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ExAC Score
Score 0.99999999936286
Ranking 93/18225 scored genes
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Sanders TADA Score
Score 0.17156909074973
Ranking 96/18665 scored genes
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Zhang D Score
Score 0.56077581741505
Ranking 207/20870 scored genes
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