Human Gene Module / Chromosome 2 / EPC2

EPC2Enhancer of polycomb homolog 2 (Drosophila)

SFARI Gene Score
2
Strong Candidate Criteria 2.1
Autism Reports / Total Reports
2 / 6
Rare Variants / Common Variants
7 / 0
Aliases
EPC2, DKFZp566F2124,  EPC-LIKE
Associated Syndromes
-
Chromosome Band
2q23.1
Associated Disorders
ASD
Relevance to Autism

EPC2 is frequently deleted along with MBD5 in cases with 2q23.1 microdeletion syndrome. While MBD5 is generally thought to be the casual locus of the syndrome, EPC2 may be responsible in part for the broader phentoype observed in patients with larger 2q23.1 deletions compared to those patients with a deletion of MBD5 only.

Molecular Function

EPC2 belongs to the enhancer of polycomb family and may play a role in transcription or DNA repair.

External Links
Gene CardOpen Targets PlatformgnomAD browserPubMed
Human
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SFARI Genomic Platforms
GPF browser SFARI genome browser
Reports related to EPC2 (6 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Primary 2q23.1 microdeletion identified by array comparative genomic hybridisation: an emerging phenotype with Angelman-like features? Jaillard S , et al. (2008) No Autistic behavior
2 Support The 2q23.1 microdeletion syndrome: clinical and behavioural phenotype van Bon BW , et al. (2009) No -
3 Highly Cited Haploinsufficiency of MBD5 associated with a syndrome involving microcephaly, intellectual disabilities, severe speech impairment, and seizures Williams SR , et al. (2009) No -
4 Support 2q23.1 microdeletion of the MBD5 gene in a female with seizures, developmental delay and distinct dysmorphic features Noh GJ and Graham JM Jr (2011) No -
5 Support - Tuncay IO et al. (2022) Yes -
6 Support - Zhou X et al. (2022) Yes -
Rare Variants   (7)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
- - copy_number_loss De novo - - 18812405 Jaillard S , et al. (2008)
- - copy_number_loss De novo - - 19809484 van Bon BW , et al. (2009)
- - copy_number_loss De novo - - 22085995 Noh GJ and Graham JM Jr (2011)
c.574C>G p.Pro192Ala missense_variant De novo - - 35982159 Zhou X et al. (2022)
c.2410A>G p.Met804Val missense_variant De novo - - 35982159 Zhou X et al. (2022)
c.2352-3T>C - splice_region_variant De novo - Multiplex 35982159 Zhou X et al. (2022)
c.1502A>G p.Asn501Ser missense_variant Familial Both parents Simplex 35190550 Tuncay IO et al. (2022)
Common Variants  

No common variants reported.

SFARI Gene score
2

Strong Candidate

EPC2 is frequently deleted along with MBD5 in cases with 2q23.1 microdeletion syndrome. While MBD5 is generally thought to be the casual locus of the syndrome, EPC2 may be responsible in part for the broader phentoype observed in patients with larger 2q23.1 deletions compared to those patients with a deletion of MBD5 only. For example, speech and language issues may be more severe with EPC2-containing deletions (PMID 19809484), although no single-gene deletions have been reported.

Score Delta: Score remained at 2

criteria met
See SFARI Gene'scoring criteria
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.

4/1/2022
3
icon
2

Decreased from 3 to 2

Description

EPC2 is frequently deleted along with MBD5 in cases with 2q23.1 microdeletion syndrome. While MBD5 is generally thought to be the casual locus of the syndrome, EPC2 may be responsible in part for the broader phentoype observed in patients with larger 2q23.1 deletions compared to those patients with a deletion of MBD5 only. For example, speech and language issues may be more severe with EPC2-containing deletions (PMID 19809484), although no single-gene deletions have been reported.

10/1/2019
4
icon
3

Decreased from 4 to 3

New Scoring Scheme
Description

EPC2 is frequently deleted along with MBD5 in cases with 2q23.1 microdeletion syndrome. While MBD5 is generally thought to be the casual locus of the syndrome, EPC2 may be responsible in part for the broader phentoype observed in patients with larger 2q23.1 deletions compared to those patients with a deletion of MBD5 only. For example, speech and language issues may be more severe with EPC2-containing deletions (PMID 19809484), although no single-gene deletions have been reported.

Reports Added
[New Scoring Scheme]
7/1/2014
No data
icon
4

Increased from No data to 4

Description

EPC2 is frequently deleted along with MBD5 in cases with 2q23.1 microdeletion syndrome. While MBD5 is generally thought to be the casual locus of the syndrome, EPC2 may be responsible in part for the broader phentoype observed in patients with larger 2q23.1 deletions compared to those patients with a deletion of MBD5 only. For example, speech and language issues may be more severe with EPC2-containing deletions (PMID 19809484), although no single-gene deletions have been reported.

4/1/2014
No data
icon
4

Increased from No data to 4

Description

EPC2 is frequently deleted along with MBD5 in cases with 2q23.1 microdeletion syndrome. While MBD5 is generally thought to be the casual locus of the syndrome, EPC2 may be responsible in part for the broader phentoype observed in patients with larger 2q23.1 deletions compared to those patients with a deletion of MBD5 only. For example, speech and language issues may be more severe with EPC2-containing deletions (PMID 19809484), although no single-gene deletions have been reported.

Krishnan Probability Score

Score 0.49790085829429

Ranking 2319/25841 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 0.99995236045916

Ranking 580/18225 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 0.94187788883153

Ranking 15096/18665 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 0.62889076434304

Ranking 38/20870 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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