EYA2

EYA transcriptional coactivator and phosphatase 2, the group of EYA transcriptional coactivator and phosphatases|MicroRNA protein coding host genes

Basic information

Region (hg38): 20:46894624-47188844

Links

ENSG00000064655 ∙ NCBI:2139 ∙ OMIM:601654 ∙ HGNC:3520 ∙ Uniprot:O00167 ∙ 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 EYA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EYA2 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				1		1
missense			31		2	33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	1	2

Variants in EYA2

This is a list of pathogenic ClinVar variants found in the EYA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-46990081-G-A		not specified	Uncertain significance (Jun 29, 2023)
20-46990108-G-A		not specified	Uncertain significance (Dec 08, 2023)
20-47001440-C-T		not specified	Uncertain significance (Apr 22, 2022)
20-47004952-C-A		not specified	Uncertain significance (Dec 06, 2022)
20-47005009-A-G		not specified	Uncertain significance (Apr 07, 2022)
20-47005048-C-T		not specified	Uncertain significance (Apr 05, 2023)
20-47005063-G-A			Benign (Apr 16, 2018)
20-47072204-A-C		not specified	Uncertain significance (Oct 10, 2023)
20-47072244-G-A		not specified	Uncertain significance (Jun 23, 2023)
20-47074198-C-T		not specified	Uncertain significance (Aug 30, 2022)
20-47074209-G-C		not specified	Uncertain significance (Feb 27, 2023)
20-47074211-C-T			Likely benign (Jul 01, 2022)
20-47074225-C-T		not specified	Uncertain significance (Dec 22, 2023)
20-47074258-C-T		not specified	Uncertain significance (May 16, 2022)
20-47074281-G-A		not specified	Uncertain significance (Jan 05, 2022)
20-47074305-G-A		not specified	Uncertain significance (Sep 22, 2023)
20-47089289-A-G			Benign (Apr 16, 2018)
20-47089302-A-G		not specified	Uncertain significance (Feb 05, 2024)
20-47089328-G-T		Hereditary breast ovarian cancer syndrome • not specified	Uncertain significance (Aug 12, 2021)
20-47089367-G-A		not specified	Uncertain significance (Mar 03, 2022)
20-47089370-A-G		not specified	Uncertain significance (Jan 04, 2024)
20-47097094-G-A		not specified	Uncertain significance (Oct 06, 2021)
20-47097133-T-A		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
20-47143066-C-T		not specified	Uncertain significance (Jan 03, 2022)
20-47143074-G-A		not specified	Uncertain significance (Nov 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EYA2	protein_coding	protein_coding	ENST00000327619	15	294230

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0980	0.902	125733	0	14	125747	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.20	272	334	0.815	0.0000205	3482
Missense in Polyphen		92	152.9	0.60171		1601
Synonymous	0.622	132	141	0.933	0.00000987	1058
Loss of Function	3.82	8	30.9	0.259	0.00000149	341

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000272	0.000272
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.000163	0.000163
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions both as protein phosphatase and as transcriptional coactivator for SIX1, and probably also for SIX2, SIX4 and SIX5 (PubMed:12500905, PubMed:23435380). Tyrosine phosphatase that dephosphorylates 'Tyr-142' of histone H2AX (H2AXY142ph) and promotes efficient DNA repair via the recruitment of DNA repair complexes containing MDC1. 'Tyr-142' phosphorylation of histone H2AX plays a central role in DNA repair and acts as a mark that distinguishes between apoptotic and repair responses to genotoxic stress (PubMed:19351884). Its function as histone phosphatase may contribute to its function in transcription regulation during organogenesis. Plays an important role in hypaxial muscle development together with SIX1 and DACH2; in this it is functionally redundant with EYA1 (PubMed:12500905). {ECO:0000269|PubMed:12500905, ECO:0000269|PubMed:19351884, ECO:0000269|PubMed:21706047, ECO:0000269|PubMed:23435380}.
• Pathway: DNA Repair;DNA Double-Strand Break Repair;Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks;DNA Double Strand Break Response (Consensus)

Recessive Scores

• pRec: 0.149

Intolerance Scores

• loftool: 0.0996
• rvis_EVS: 0.09
• rvis_percentile_EVS: 60.65

Haploinsufficiency Scores

• pHI: 0.812
• hipred: Y
• hipred_score: 0.663
• ghis: 0.457

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.924

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Eya2

Gene ontology

• Biological process: DNA repair;mesodermal cell fate specification;striated muscle tissue development;histone dephosphorylation;peptidyl-tyrosine dephosphorylation;positive regulation of DNA repair;anatomical structure development;extrinsic apoptotic signaling pathway in absence of ligand;mitochondrial outer membrane permeabilization;negative regulation of extrinsic apoptotic signaling pathway in absence of ligand
• Cellular component: nucleus;nucleoplasm;mitochondrion;cytosol
• Molecular function: magnesium ion binding;protein tyrosine phosphatase activity;protein binding;transcription factor binding