Human Gene Module / Chromosome 15 / HERC1

HERC1HECT and RLD domain containing E3 ubiquitin protein ligase family member 1

SFARI Gene Score
2S
Strong Candidate, Syndromic Criteria 2.1, Syndromic
Autism Reports / Total Reports
7 / 14
Rare Variants / Common Variants
18 / 0
Aliases
-
Associated Syndromes
-
Chromosome Band
15q22.31
Associated Disorders
-
Relevance to Autism

De novo nonsense variants in the HERC1 gene have been identified in a Japanese ASD proband (Hashimoto et al., 2016) and in an ASD proband from the Autism Sequencing Consortium (Satterstrom et al., 2020), while an inherited nonsense variant in this gene was observed in an ASD proband from the iHART cohort (Ruzzo et al., 2019). Additional de novo variants in this gene were identified in ASD probands from the Simons Simplex Collection (Iossifov et al., 2014). Limited social interaction had previously been observed in an individual with MDFPMR (Nguyen et al., 2016). Roy et al., 2021 found that HERC1 exhibited high expression in the anterodorsal thalamus (AD) of mice, and that knockdown of HERC1 in AD thalamus resulted in memory deficits and neuronal hyperexcitability, phenotypes that were also observed in AD thalamus-specific PTCHD1 knock-down mice.

Molecular Function

This gene encodes a member of the HERC protein family. This protein stimulates guanine nucleotide exchange on ARF1 and Rab proteins. This protein may be involved in membrane transport processes. Biallelic variants in the HERC1 gene are responsible for macrocephaly, dysmorphic facies, and psychomotor retardation (MDFPMR; OMIM 617011), an autosomal recessive neurodevelopmental disorder characterized by large head and somatic overgrowth apparent at birth followed by global developmental delay (Ortega-Recalde et al., 2015; Nguyen et al., 2016; Aggarwal et al. 2016; Schwarz et al., 2020).

SFARI Genomic Platforms
Reports related to HERC1 (14 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Support The contribution of de novo coding mutations to autism spectrum disorder Iossifov I et al. (2014) Yes -
2 Support - Ortega-Recalde O et al. (2015) No Epilepsy/seizures
3 Support - Nguyen LS et al. (2016) No Limited social interaction
4 Primary Whole-exome sequencing and neurite outgrowth analysis in autism spectrum disorder Hashimoto R , et al. (2015) Yes -
5 Support - Aggarwal S et al. (2016) No -
6 Support Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks Ruzzo EK , et al. (2019) Yes -
7 Support Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism Satterstrom FK et al. (2020) Yes -
8 Support - Schwarz JM et al. (Sep-) No ADHD, epilepsy/seizures
9 Support - Roy DS et al. (2021) No -
10 Support - Woodbury-Smith M et al. (2022) Yes -
11 Recent Recommendation - Singh T et al. (2022) No -
12 Support - Zhou X et al. (2022) Yes -
13 Support - Cirnigliaro M et al. (2023) Yes -
14 Support - Thomas V Fernandez et al. (2023) No -
Rare Variants   (18)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
c.1487C>A p.Ser496Ter stop_gained De novo - - 35982159 Zhou X et al. (2022)
c.7357A>G p.Ser2453Gly missense_variant De novo - - 35982159 Zhou X et al. (2022)
c.13631T>C p.Val4544Ala missense_variant De novo - - 35982159 Zhou X et al. (2022)
c.7539C>T p.Leu2513%3D synonymous_variant De novo - - 35982159 Zhou X et al. (2022)
c.12364C>T p.Gln4122Ter stop_gained De novo - - 31981491 Satterstrom FK et al. (2020)
c.5117A>C p.Tyr1706Ser missense_variant De novo - Simplex 35982159 Zhou X et al. (2022)
c.12460A>T p.Lys4154Ter stop_gained De novo - Simplex 26582266 Hashimoto R , et al. (2015)
c.3446T>C p.Ile1149Thr missense_variant De novo - Simplex 25363768 Iossifov I et al. (2014)
c.11423A>C p.Asn3808Thr missense_variant Unknown - - 35205252 Woodbury-Smith M et al. (2022)
c.11036G>A p.Arg3679His missense_variant De novo - Simplex 25363768 Iossifov I et al. (2014)
c.11833C>T p.Gln3945Ter stop_gained Familial Maternal Multiplex 31398340 Ruzzo EK , et al. (2019)
c.9748C>T p.Arg3250Ter stop_gained Familial Both parents Simplex 26153217 Nguyen LS et al. (2016)
c.4906-2A>C - splice_site_variant Familial Both parents Multiplex 27108999 Aggarwal S et al. (2016)
c.11901+1G>A - splice_site_variant Familial Maternal Multiplex 37506195 Cirnigliaro M et al. (2023)
c.4466G>A p.Ser1489Asn missense_variant De novo - Simplex 37788244 Thomas V Fernandez et al. (2023)
c.2625G>A p.Trp875Ter stop_gained Familial Maternal Multiplex 26138117 Ortega-Recalde O et al. (2015)
14072G>C p.Arg4691Pro missense_variant Familial Both parents Multiplex 32921582 Schwarz JM et al. (Sep-)
c.13559G>A p.Gly4520Glu missense_variant Familial Paternal Multiplex 26138117 Ortega-Recalde O et al. (2015)
Common Variants  

No common variants reported.

SFARI Gene score
2S

Strong Candidate, Syndromic

Score Delta: Score remained at 2S

2

Strong Candidate

See all Category 2 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.

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
icon
2S

Increased from to 2S

Krishnan Probability Score

Score 0.4988635035882

Ranking 2206/25841 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.
ExAC Score

Score 0.99999999999837

Ranking 43/18225 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
Sanders TADA Score

Score 0.95007094492536

Ranking 18346/18665 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).
Zhang D Score

Score 0.46730431381646

Ranking 769/20870 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.
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