EMSY

EMSY transcriptional repressor, BRCA2 interacting, the group of EMSY complex

Basic information

Region (hg38): 11:76444922-76553031

Previous symbols: [ "C11orf30" ]

Links

ENSG00000158636 ∙ NCBI:56946 ∙ OMIM:608574 ∙ HGNC:18071 ∙ Uniprot:Q7Z589 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EMSY gene.

• Inborn genetic diseases (7 variants)
• not provided (6 variants)
• EMSY-related condition (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EMSY gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					2	2
missense			8		1	9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1		3	4
non coding						0
Total	0	0	8	0	3

Variants in EMSY

This is a list of pathogenic ClinVar variants found in the EMSY region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-76451851-C-T			Benign (Jun 25, 2018)
11-76451964-T-C			Benign (Jan 30, 2018)
11-76453321-A-G		not specified	Uncertain significance (Sep 15, 2021)
11-76463865-C-A			Benign (Dec 31, 2019)
11-76464057-A-G		not specified	Uncertain significance (Jun 11, 2021)
11-76496403-C-A		not specified	Uncertain significance (Aug 02, 2021)
11-76516138-G-A		EMSY-related disorder	Benign (Aug 10, 2022)
11-76523148-T-C			Benign (Feb 12, 2018)
11-76523150-C-G		EMSY-related disorder	Uncertain significance (Apr 17, 2023)
11-76528419-A-G		not specified	Uncertain significance (Sep 16, 2021)
11-76535916-T-C		EMSY-related disorder	Likely benign (Mar 16, 2022)
11-76544410-T-G			Benign (Jul 11, 2017)
11-76544468-G-A			Benign (Jul 23, 2018)
11-76544676-G-C		not specified	Uncertain significance (Jun 18, 2021)
11-76544772-C-A		not specified	Uncertain significance (Aug 17, 2021)
11-76546164-C-T		not specified	Uncertain significance (Oct 18, 2021)
11-76546171-T-C		EMSY-related disorder	Benign (Oct 27, 2021)
11-76546257-A-G		EMSY-related disorder	Uncertain significance (Oct 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EMSY	protein_coding	protein_coding	ENST00000529032	20	108103

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	2.46e-7	125742	0	6	125748	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.99	568	718	0.791	0.0000374	8547
Missense in Polyphen		143	227.25	0.62927		2710
Synonymous	-1.09	284	262	1.09	0.0000143	2782
Loss of Function	6.69	4	59.9	0.0668	0.00000298	669

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000716	0.0000716
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulator which is able to repress transcription, possibly via its interaction with a multiprotein chromatin remodeling complex that modifies the chromatin. Its interaction with BRCA2 suggests that it may play a central role in the DNA repair function of BRCA2. As part of a histone H3-specific methyltransferase complex may mediate ligand-dependent transcriptional activation by nuclear hormone receptors. {ECO:0000269|PubMed:14651845, ECO:0000269|PubMed:19131338}.
• Pathway: Mesodermal Commitment Pathway (Consensus)

Recessive Scores

• pRec: 0.117

Intolerance Scores

• rvis_EVS: -1.95
• rvis_percentile_EVS: 1.88

Haploinsufficiency Scores

• pHI: 0.594
• hipred: Y
• hipred_score: 0.794
• ghis: 0.674

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Emsy

Gene ontology

• Biological process: DNA repair;chromatin organization;regulation of transcription, DNA-templated
• Cellular component: nucleoplasm
• Molecular function: protein binding;protein homodimerization activity