EMSY
protein-codingEMSY transcriptional repressor, BRCA2 interacting, the group of EMSY complex
Gene summary
Predicted to enable identical protein binding activity. Predicted to be involved in several processes, including DNA repair; DNA-templated transcription; and regulation of DNA-templated transcription. Located in nucleoplasm. Implicated in allergic rhinitis and asthma. [provided by Alliance of Genome Resources, Jun 2026]
- C11orf30
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~108.1 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to EMSY variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001300942.2. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 2 | 3 | |||
| missense | 16 | 2 | 1 | 19 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 22 | 2 | 3 | 27 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001287871.1 | 21 | MANE Select | |
| Ensembl | ENSP00000511840.1 | 21 | MANE Select | |
| RefSeq | NP_001287872.1 | 20 | Standard | |
| RefSeq | NP_001287873.1 | 20 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Mesodermal Commitment Pathway
Biological Process
- DNA repair
- chromatin organization
- regulation of transcription, DNA-templated
Molecular Function
- protein binding
- protein homodimerization activity
Cellular Component
- nucleoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000529032
- Coding exons
- 20
- Length
- 108103
- Individuals with no LoFs
- 125742
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 6
- Defined
- 125748
- p
- 0.0000239
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.99 | 568 | 718 | 0.791 | 0.0000374 | 8547 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000072 | 0.000058 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000018 | 0.000018 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- 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}.;
Recessive Scores
- pRec
- 0.117
Intolerance Scores
- RVIS EVS
- -1.95
- RVIS percentile EVS
- 1.88
Essentials
- Essential (gene trap)
- N