Human Gene Module / Chromosome 17 / CHD3

CHD3chromodomain helicase DNA binding protein 3

SFARI Gene Score
1S
High Confidence, Syndromic Criteria 1.1, Syndromic
Autism Reports / Total Reports
12 / 28
Rare Variants / Common Variants
122 / 0
Aliases
CHD3, Mi-2a,  Mi2-ALPHA,  ZFH
Associated Syndromes
Snijders Blok-Campeau syndrome (SNIBCPS), Snijders Blok-Campeau syndrome, ASD, DD, ID, Snijders Blok-Campeau syndrome, DD, Snijders Blok-Campeau syndrome, ASD, DD, Snijders Blok-Campeau syndrome, DD, ID, Snijders Blok-Campeau syndrome, ASD, DD, epilepsy/, Snijders Blok-Campeau syndrome
Chromosome Band
17p13.1
Associated Disorders
ASD
Relevance to Autism

Two de novo missense variants and one de novo in-frame deletion variant were identified in the CHD3 gene in ASD probands following whole-exome or whole-genome sequencing (Iossifov et al., 2014; Yuen et al., 2016; Yuen et al., 2017). Snijders Blok et al., 2018 described a cohort of 35 individuals with de novo CHD3 mutations and overlapping phenotypes, including developmental delay/intellectual disability and speech delay/disorder; nine individuals (29%) displayed autism or autistic features, including stereotypic and hand-flapping behavior.

Molecular Function

This gene encodes a member of the CHD family of proteins which are characterized by the presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. This protein is one of the components of a histone deacetylase complex referred to as the Mi-2/NuRD complex which participates in the remodeling of chromatin by deacetylating histones. Chromatin remodeling is essential for many processes including transcription.

External Links
Gene CardOpen Targets PlatformgnomAD browserPubMed
Human
Entrez GeneOMIMUniProtHumanBaseVariCarta
SFARI Genomic Platforms
GPF browser SFARI genome browser
Reports related to CHD3 (28 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Primary The contribution of de novo coding mutations to autism spectrum disorder Iossifov I et al. (2014) Yes -
2 Support Genome-wide characteristics of de novo mutations in autism Yuen RK et al. (2016) Yes -
3 Support Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder C Yuen RK et al. (2017) Yes -
4 Support Rates, distribution and implications of postzygotic mosaic mutations in autism spectrum disorder Lim ET , et al. (2017) Yes -
5 Recent Recommendation CHD3 helicase domain mutations cause a neurodevelopmental syndrome with macrocephaly and impaired speech and language Snijders Blok L , et al. (2018) No ASD or autistic features
6 Support Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks Ruzzo EK , et al. (2019) Yes -
7 Support Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes Feliciano P et al. (2019) Yes -
8 Recent Recommendation A second cohort of CHD3 patients expands the molecular mechanisms known to cause Snijders Blok-Campeau syndrome Drivas TG et al. (2020) No Autistic features
9 Recent recommendation - Sadler B et al. (2021) No -
10 Support - Mizukami M et al. (2021) Yes -
11 Recent Recommendation - van der Spek J et al. (2022) No ASD or autistic features, ID
12 Support - Zhou X et al. (2022) Yes -
13 Support - LeBreton L et al. (2023) Yes -
14 Recent Recommendation - Timberlake AT et al. (2023) No -
15 Support - Sheth F et al. (2023) Yes DD, ID
16 Support - Patricia Pascual et al. (2023) No ASD, ADHD
17 Support - Ashraf Yahia et al. (2024) No -
18 Support - Noor Smal et al. () No -
19 Support - Tomoki T Nomakuchi et al. () Yes -
20 Support - Axel Schmidt et al. (2024) No ID
21 Support - Yuanyuan Gao et al. (2024) No ASD
22 Support - Liene Thys et al. (2024) No DD, ID
23 Support - Hosneara Akter et al. () No ID, epilepsy/seizures, autistic behavior
24 Support - Xiaoling Tie et al. () No ASD
25 Support - Yumi Enomoto et al. () No Autistic features
26 Support - Anca Ionescu et al. () No ASD or ASD traits
27 Support - Evgeny N Suspitsin et al. (2025) Yes ID
28 Recent Recommendation - Kan Yang et al. (2026) No ASD or autistic features, DD, ID
Rare Variants   (122)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
- - copy_number_loss De novo - Simplex 32483341 Drivas TG et al. (2020)
- - copy_number_gain Unknown - Multiplex 32483341 Drivas TG et al. (2020)
- p.Glu315Lys missense_variant De novo - Simplex 28714951 Lim ET , et al. (2017)
c.5590+1G>T p.? splice_site_variant De novo - - 39542866 Xiaoling Tie et al. ()
c.1120G>A p.Glu374Lys missense_variant De novo - - 35982159 Zhou X et al. (2022)
c.2464A>T p.Met822Leu missense_variant De novo - - 35982159 Zhou X et al. (2022)
c.3131G>A p.Arg1044Gln missense_variant De novo - - 35982159 Zhou X et al. (2022)
c.3691C>T p.Arg1231Trp missense_variant De novo - - 35982159 Zhou X et al. (2022)
c.5307T>C p.Asn1769= synonymous_variant De novo - - 35982159 Zhou X et al. (2022)
c.292G>A p.Gly98Arg missense_variant Unknown - - 39342494 Hosneara Akter et al. ()
c.3505C>T p.Arg1169Trp missense_variant De novo - - 39542866 Xiaoling Tie et al. ()
c.1099G>A p.Gly367Arg missense_variant Unknown - - 39342494 Hosneara Akter et al. ()
c.1618C>T p.Arg540Cys missense_variant Unknown - - 39342494 Hosneara Akter et al. ()
c.2197G>A p.Gly733Arg missense_variant Unknown - - 39342494 Hosneara Akter et al. ()
c.5432G>A p.Arg1811Gln missense_variant De novo - - 36565043 LeBreton L et al. (2023)
c.3691C>T p.Arg1231Trp missense_variant De novo - - 39213953 Liene Thys et al. (2024)
c.1796G>A p.Arg599His missense_variant De novo - - 31452935 Feliciano P et al. (2019)
c.473C>A p.Pro158Gln missense_variant De novo - - 39039281 Axel Schmidt et al. (2024)
c.1495C>T p.Arg499Ter stop_gained De novo - - 37761804 Patricia Pascual et al. (2023)
c.3551T>G p.Phe1184Cys missense_variant De novo - Simplex 38965372 Noor Smal et al. ()
c.3515G>A p.Arg1172Gln missense_variant De novo - - 39039281 Axel Schmidt et al. (2024)
c.3536A>T p.Asp1179Val missense_variant Unknown - - 39039281 Axel Schmidt et al. (2024)
c.4202G>A p.Arg1401Gln missense_variant Unknown - - 39039281 Axel Schmidt et al. (2024)
c.1708-1G>T - splice_site_variant Unknown - Simplex 39050258 Yuanyuan Gao et al. (2024)
c.2902C>G p.Leu968Val missense_variant De novo - Simplex 27525107 Yuen RK et al. (2016)
c.6068A>G p.Asn2023Ser missense_variant Unknown - Simplex 37543562 Sheth F et al. (2023)
c.2881G>C p.Gly961Arg missense_variant De novo - Simplex 39988727 Yumi Enomoto et al. ()
c.4073-3_4078del - splice_site_variant De novo - Simplex 32483341 Drivas TG et al. (2020)
c.5812G>A p.Ala1938Thr missense_variant De novo - - 39031459 Tomoki T Nomakuchi et al. ()
c.3482A>T p.His1161Leu missense_variant De novo - Simplex 39988727 Yumi Enomoto et al. ()
c.3505C>T p.Arg1169Trp missense_variant De novo - Simplex 39988727 Yumi Enomoto et al. ()
c.2657A>G p.His886Arg missense_variant De novo - Simplex 32483341 Drivas TG et al. (2020)
c.2749A>T p.Asn917Tyr missense_variant De novo - Simplex 32483341 Drivas TG et al. (2020)
c.2831T>A p.Phe944Tyr missense_variant De novo - Simplex 32483341 Drivas TG et al. (2020)
c.2842T>C p.Ser948Pro missense_variant De novo - Simplex 32483341 Drivas TG et al. (2020)
c.2896C>T p.Arg966Trp missense_variant De novo - Simplex 32483341 Drivas TG et al. (2020)
c.2897G>C p.Arg966Pro missense_variant De novo - Simplex 32483341 Drivas TG et al. (2020)
c.2905A>G p.Lys969Glu missense_variant De novo - Simplex 32483341 Drivas TG et al. (2020)
c.2954G>A p.Arg985Gln missense_variant De novo - - 37761804 Patricia Pascual et al. (2023)
c.3073C>T p.Arg1025Trp missense_variant De novo - Simplex 32483341 Drivas TG et al. (2020)
c.3239T>A p.Leu1080His missense_variant De novo - Simplex 32483341 Drivas TG et al. (2020)
c.3515G>A p.Arg1172Gln missense_variant De novo - Simplex 32483341 Drivas TG et al. (2020)
c.3784C>T p.Arg1262Trp missense_variant De novo - Simplex 32483341 Drivas TG et al. (2020)
c.4243C>T p.Arg1415Cys missense_variant De novo - Simplex 32483341 Drivas TG et al. (2020)
c.5863G>T p.Ala1955Ser missense_variant De novo - Simplex 32483341 Drivas TG et al. (2020)
c.2896C>T p.Arg966Trp missense_variant De novo - Simplex 33358638 Mizukami M et al. (2021)
c.3130C>T p.Arg1044Trp missense_variant De novo - - 37761804 Patricia Pascual et al. (2023)
c.3209G>A p.Gly1070Asp missense_variant De novo - - 37761804 Patricia Pascual et al. (2023)
c.3406A>C p.Thr1136Pro missense_variant De novo - - 37761804 Patricia Pascual et al. (2023)
c.3505C>T p.Arg1169Trp missense_variant De novo - - 37761804 Patricia Pascual et al. (2023)
c.3506G>A p.Arg1169Gln missense_variant De novo - - 37761804 Patricia Pascual et al. (2023)
c.3541A>T p.Ile1181Phe missense_variant De novo - - 37761804 Patricia Pascual et al. (2023)
c.3673G>C p.Ala1225Pro missense_variant De novo - - 37761804 Patricia Pascual et al. (2023)
c.3683G>A p.Arg1228Gln missense_variant De novo - - 37761804 Patricia Pascual et al. (2023)
c.3865G>A p.Ala1289Thr missense_variant Unknown - - 37761804 Patricia Pascual et al. (2023)
c.4073-2A>G - splice_site_variant De novo - Simplex 30397230 Snijders Blok L , et al. (2018)
c.5452C>T p.Arg1818Trp missense_variant De novo - Simplex 25363768 Iossifov I et al. (2014)
c.1369G>T p.Glu457Ter stop_gained De novo - Simplex 30397230 Snijders Blok L , et al. (2018)
c.5642G>T p.Arg1881Leu missense_variant De novo - - 41255692 Evgeny N Suspitsin et al. (2025)
c.5360A>G p.Glu1787Gly missense_variant Familial - Multiplex 39988727 Yumi Enomoto et al. ()
c.3509C>T p.Thr1170Met missense_variant De novo - Multiplex 31398340 Ruzzo EK , et al. (2019)
c.2954G>C p.Arg985Pro missense_variant De novo - Simplex 39050258 Yuanyuan Gao et al. (2024)
c.3371C>T p.Ala1124Val missense_variant De novo - Simplex 39050258 Yuanyuan Gao et al. (2024)
c.4280G>A p.Trp1427Ter stop_gained Familial Maternal Simplex 32483341 Drivas TG et al. (2020)
c.2284_2286del p.Lys762del inframe_deletion De novo - Simplex 28263302 C Yuen RK et al. (2017)
c.2953C>T p.Leu985= missense_variant De novo - Simplex 30397230 Snijders Blok L , et al. (2018)
c.3784_3786del p.Met1262del inframe_deletion De novo - Simplex 32483341 Drivas TG et al. (2020)
c.3325_3327del p.Tyr1109del inframe_deletion De novo - - 37761804 Patricia Pascual et al. (2023)
c.3502_3504del p.Ser1168del inframe_deletion De novo - - 37761804 Patricia Pascual et al. (2023)
c.3477C>A p.Gly1159= missense_variant De novo - Simplex 30397230 Snijders Blok L , et al. (2018)
c.2657A>G p.His886Arg missense_variant De novo - Simplex 30397230 Snijders Blok L , et al. (2018)
c.2745G>T p.Leu915Phe missense_variant De novo - Simplex 30397230 Snijders Blok L , et al. (2018)
c.2761G>A p.Glu921Lys missense_variant De novo - Simplex 30397230 Snijders Blok L , et al. (2018)
c.2882G>A p.Gly961Glu missense_variant De novo - Simplex 30397230 Snijders Blok L , et al. (2018)
c.2954G>A p.Arg985Gln missense_variant De novo - Simplex 30397230 Snijders Blok L , et al. (2018)
c.3362G>C p.Arg1121Pro missense_variant De novo - Simplex 30397230 Snijders Blok L , et al. (2018)
c.3407C>T p.Thr1136Ile missense_variant De novo - Simplex 30397230 Snijders Blok L , et al. (2018)
c.3472T>C p.Trp1158Arg missense_variant De novo - Simplex 30397230 Snijders Blok L , et al. (2018)
c.3505C>T p.Arg1169Trp missense_variant De novo - Simplex 30397230 Snijders Blok L , et al. (2018)
c.3512A>G p.His1171Arg missense_variant De novo - Simplex 30397230 Snijders Blok L , et al. (2018)
c.3515G>A p.Arg1172Gln missense_variant De novo - Simplex 30397230 Snijders Blok L , et al. (2018)
c.3560G>C p.Arg1187Pro missense_variant De novo - Simplex 30397230 Snijders Blok L , et al. (2018)
c.3707T>C p.Leu1236Pro missense_variant De novo - Simplex 30397230 Snijders Blok L , et al. (2018)
c.4025G>A p.Arg1342Gln missense_variant De novo - Simplex 30397230 Snijders Blok L , et al. (2018)
c.5642G>T p.Arg1881Leu missense_variant De novo - Simplex 30397230 Snijders Blok L , et al. (2018)
c.1384del p.Cys462AlafsTer22 frameshift_variant Unknown - Simplex 32483341 Drivas TG et al. (2020)
c.1795dup p.Arg599ProfsTer47 frameshift_variant Unknown - Simplex 32483341 Drivas TG et al. (2020)
c.4532_4535del p.Phe1511TrpfsTer31 frameshift_variant De novo - - 31452935 Feliciano P et al. (2019)
c.3473G>A p.Trp1158Ter stop_gained Familial Maternal Simplex 35346573 van der Spek J et al. (2022)
c.3910C>T p.Arg1304Ter stop_gained Familial Maternal Simplex 35346573 van der Spek J et al. (2022)
c.4151C>G p.Ser1384Ter stop_gained Familial Maternal Simplex 35346573 van der Spek J et al. (2022)
c.4280G>A p.Trp1427Ter stop_gained Familial Maternal Simplex 35346573 van der Spek J et al. (2022)
c.4312C>T p.Gln1438Ter stop_gained Familial Paternal Simplex 35346573 van der Spek J et al. (2022)
c.5089C>T p.Arg1697Ter stop_gained Familial Maternal Simplex 35346573 van der Spek J et al. (2022)
c.5461G>T p.Glu1821Ter stop_gained Familial Maternal Simplex 35346573 van der Spek J et al. (2022)
c.3725G>A p.Arg1242Gln missense_variant Familial Paternal - 37761804 Patricia Pascual et al. (2023)
c.2422_3155+60del - frameshift_variant Familial Paternal Simplex 35346573 van der Spek J et al. (2022)
c.3325_3327del p.Tyr1109del inframe_deletion De novo - Simplex 30397230 Snijders Blok L , et al. (2018)
c.3357_3358inv p.Lys1120Gln missense_variant De novo - Simplex 30397230 Snijders Blok L , et al. (2018)
c.5767+33_5767+34insAACG - frameshift_variant De novo - Simplex 30397230 Snijders Blok L , et al. (2018)
c.3603_3614del p.Met1202_Thr1205del inframe_deletion De novo - Simplex 32483341 Drivas TG et al. (2020)
c.2327A>G p.Asp776Gly missense_variant Familial Paternal Multiplex 38300321 Ashraf Yahia et al. (2024)
c.1888T>C p.Trp630Arg missense_variant Familial Paternal Simplex 35346573 van der Spek J et al. (2022)
c.2497T>C p.Phe833Leu missense_variant Familial Maternal Simplex 35346573 van der Spek J et al. (2022)
c.2617G>A p.Gly873Ser missense_variant Familial Paternal Simplex 35346573 van der Spek J et al. (2022)
c.2947A>G p.Ile983Val missense_variant Familial Maternal Simplex 35346573 van der Spek J et al. (2022)
c.3137C>T p.Pro1046Leu missense_variant Familial Maternal Simplex 35346573 van der Spek J et al. (2022)
c.3373C>G p.Pro1125Ala missense_variant Familial Maternal Simplex 35346573 van der Spek J et al. (2022)
c.4025G>A p.Arg1342Gln missense_variant Familial Paternal Simplex 35346573 van der Spek J et al. (2022)
c.4456C>G p.Gln1486Glu missense_variant Familial Paternal Simplex 35346573 van der Spek J et al. (2022)
c.5117G>A p.Arg1706Gln missense_variant Familial Maternal Simplex 35346573 van der Spek J et al. (2022)
c.5276G>A p.Arg1759Gln missense_variant Familial Maternal Simplex 35346573 van der Spek J et al. (2022)
c.5509G>A p.Glu1837Lys missense_variant Familial Maternal Simplex 35346573 van der Spek J et al. (2022)
c.5915A>C p.Lys1972Thr missense_variant Familial Maternal Simplex 35346573 van der Spek J et al. (2022)
c.5184_5185del p.Asp1730PhefsTer10 frameshift_variant De novo - - 37761804 Patricia Pascual et al. (2023)
c.1430C>T p.Ser477Phe missense_variant Familial Paternal Multiplex 35346573 van der Spek J et al. (2022)
c.2953C>T p.Leu985= missense_variant Familial Maternal Multiplex 30397230 Snijders Blok L , et al. (2018)
c.3592_3606del p.Ala1198_Met1202del inframe_deletion De novo - Simplex 39050258 Yuanyuan Gao et al. (2024)
c.5663G>A p.Arg1888Gln missense_variant Familial Maternal Multiplex 35346573 van der Spek J et al. (2022)
c.4042G>A p.Ala1348Thr missense_variant Familial Maternal Multiplex 37761804 Patricia Pascual et al. (2023)
c.1706A>G p.Gln569Arg missense_variant De novo - Multiplex (monozygotic twins) 32483341 Drivas TG et al. (2020)
c.3482A>G p.Lys1161Arg missense_variant De novo - Multiplex (monozygotic twins) 30397230 Snijders Blok L , et al. (2018)
Common Variants  

No common variants reported.

SFARI Gene score
1S

High Confidence, Syndromic

Score Delta: Score remained at 1S

criteria met
See SFARI Gene'scoring criteria
1

High Confidence

See all Category 1 Genes

We 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.

S

Syndromic

See all Category S Genes

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."

1/1/2021
1
icon
1

Score remained at 1

Description

Two de novo missense variants and one de novo in-frame deletion variant were identified in the CHD3 gene in ASD probands following whole-exome or whole-genome sequencing (Iossifov et al., 2014; Yuen et al., 2016; Yuen et al., 2017). Snijders Blok et al., 2018 described a cohort of 35 individuals with de novo CHD3 mutations and overlapping phenotypes, including developmental delay/intellectual disability and speech delay/disorder; nine individuals (29%) displayed autism or autistic features, including stereotypic and hand-flapping behavior.

Reports Added
[Rates, distribution and implications of postzygotic mosaic mutations in autism spectrum disorder.2017] [Rare and de novo coding variants in chromodomain genes in Chiari I malformation2021] [A de novo CHD3 variant in a child with intellectual disability, autism, joint laxity, and dysmorphisms2021]
4/1/2020
1
icon
1

Score remained at 1

Description

Two de novo missense variants and one de novo in-frame deletion variant were identified in the CHD3 gene in ASD probands following whole-exome or whole-genome sequencing (Iossifov et al., 2014; Yuen et al., 2016; Yuen et al., 2017). Snijders Blok et al., 2018 described a cohort of 35 individuals with de novo CHD3 mutations and overlapping phenotypes, including developmental delay/intellectual disability and speech delay/disorder; nine individuals (29%) displayed autism or autistic features, including stereotypic and hand-flapping behavior.

Reports Added
[A second cohort of CHD3 patients expands the molecular mechanisms known to cause Snijders Blok-Campeau syndrome2020]
10/1/2019
4S
icon
1

Decreased from 4S to 1

New Scoring Scheme
Description

Two de novo missense variants and one de novo in-frame deletion variant were identified in the CHD3 gene in ASD probands following whole-exome or whole-genome sequencing (Iossifov et al., 2014; Yuen et al., 2016; Yuen et al., 2017). Snijders Blok et al., 2018 described a cohort of 35 individuals with de novo CHD3 mutations and overlapping phenotypes, including developmental delay/intellectual disability and speech delay/disorder; nine individuals (29%) displayed autism or autistic features, including stereotypic and hand-flapping behavior.

Reports Added
[Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes2019] [New Scoring Scheme]
7/1/2019
4S
icon
4S

Decreased from 4S to 4S

Description

Two de novo missense variants and one de novo in-frame deletion variant were identified in the CHD3 gene in ASD probands following whole-exome or whole-genome sequencing (Iossifov et al., 2014; Yuen et al., 2016; Yuen et al., 2017). Snijders Blok et al., 2018 described a cohort of 35 individuals with de novo CHD3 mutations and overlapping phenotypes, including developmental delay/intellectual disability and speech delay/disorder; nine individuals (29%) displayed autism or autistic features, including stereotypic and hand-flapping behavior.

Reports Added
[Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks.2019]
10/1/2018
icon
4S

Increased from to 4S

Description

Two de novo missense variants and one de novo in-frame deletion variant were identified in the CHD3 gene in ASD probands following whole-exome or whole-genome sequencing (Iossifov et al., 2014; Yuen et al., 2016; Yuen et al., 2017). Snijders Blok et al., 2018 described a cohort of 35 individuals with de novo CHD3 mutations and overlapping phenotypes, including developmental delay/intellectual disability and speech delay/disorder; nine individuals (29%) displayed autism or autistic features, including stereotypic and hand-flapping behavior.

Krishnan Probability Score

Score 0.50356225951409

Ranking 1941/25841 scored genes


[Show Scoring Methodology]
Krishnan and colleagues generated probability scores genome-wide by using a machine learning approach on a human brain-specific gene network. The method was first presented in Nat Neurosci 19, 1454-1462 (2016), and scores for more than 25,000 RefSeq genes can be accessed in column G of supplementary table 3 (see: http://www.nature.com/neuro/journal/v19/n11/extref/nn.4353-S5.xlsx). A searchable browser, with the ability to view networks of associated ASD risk genes, can be found at asd.princeton.edu.
Original Source
ExAC Score

Score 0.99999999551797

Ranking 123/18225 scored genes


[Show Scoring Methodology]
The Exome Aggregation Consortium (ExAC) is a summary database of 60,706 exomes that has been widely used to estimate 'constraint' on mutation for individual genes. It was introduced by Lek et al. Nature 536, 285-291 (2016), and the ExAC browser can be found at exac.broadinstitute.org. The pLI score was developed as measure of intolerance to loss-of- function mutation. A pLI > 0.9 is generally viewed as highly constrained, and thus any loss-of- function mutations in autism in such a gene would be more likely to confer risk. For a full list of pLI scores see: ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3.1/functional_gene_constraint/fordist_cle aned_exac_nonTCGA_z_pli_rec_null_data.txt
Original Source
Sanders TADA Score

Score 0.90096203965782

Ranking 6477/18665 scored genes


[Show Scoring Methodology]
The TADA score ('Transmission and De novo Association') was introduced by He et al. PLoS Genet 9(8):e1003671 (2013), and is a statistic that integrates evidence from both de novo and transmitted mutations. It forms the basis for the claim of 65 individual genes being strongly associated with autism risk at a false discovery rate of 0.1 (Sanders et al. Neuron 87, 1215-1233 (2015)). The calculated TADA score for 18,665 RefSeq genes can be found in column P of Supplementary Table 6 in the Sanders et al. paper (the column headed 'tadaFdrAscSscExomeSscAgpSmallDel'), which represents a combined analysis of exome data and small de novo deletions (see www.cell.com/cms/attachment/2038545319/2052606711/mmc7.xlsx).
Original Source
Zhang D Score

Score 0.50767055769192

Ranking 472/20870 scored genes


[Show Scoring Methodology]
The DAMAGES score (disease-associated mutation analysis using gene expression signatures), or D score, was developed to combine evidence from de novo loss-of- function mutation with evidence from cell-type- specific gene expression in the mouse brain (specifically translational profiles of 24 specific mouse CNS cell types isolated from 6 different brain regions). Genes with positive D scores are more likely to be associated with autism risk, with higher-confidence genes having higher D scores. This statistic was first presented by Zhang & Shen (Hum Mutat 38, 204- 215 (2017), and D scores for more than 20,000 RefSeq genes can be found in column M in supplementary table 2 from that paper.
Original Source
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