ETAA1

ETAA1 activator of ATR kinase

Basic information

Region (hg38): 2:67397322-67412089

Links

ENSG00000143971 ∙ NCBI:54465 ∙ OMIM:613196 ∙ HGNC:24648 ∙ Uniprot:Q9NY74 ∙ 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 ETAA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ETAA1 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					3	3
missense			43	5		48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	43	5	3

Variants in ETAA1

This is a list of pathogenic ClinVar variants found in the ETAA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-67397454-T-G		not specified	Uncertain significance (Jun 27, 2022)
2-67397495-C-T		not specified	Uncertain significance (Oct 27, 2021)
2-67397496-G-T			Benign (Feb 25, 2018)
2-67397531-C-T		not specified	Uncertain significance (May 26, 2022)
2-67397539-G-A		not specified	Uncertain significance (May 24, 2024)
2-67397542-C-G		not specified	Uncertain significance (Apr 08, 2024)
2-67397563-T-C		not specified	Uncertain significance (Nov 19, 2022)
2-67397567-C-T		not specified	Uncertain significance (Aug 14, 2023)
2-67397572-G-A		not specified	Uncertain significance (Feb 06, 2023)
2-67397580-G-C		not specified	Uncertain significance (Oct 16, 2024)
2-67397582-C-T		not specified	Likely benign (Feb 10, 2022)
2-67397585-G-T		not specified	Uncertain significance (Sep 16, 2021)
2-67397593-A-G		not specified	Likely benign (Feb 07, 2023)
2-67397630-A-G		not specified	Uncertain significance (Jun 03, 2024)
2-67399192-G-C		not specified	Uncertain significance (Jul 08, 2022)
2-67399205-A-C		not specified	Uncertain significance (Apr 18, 2023)
2-67399258-A-G		not specified	Uncertain significance (Jul 20, 2021)
2-67399550-G-C		not specified	Uncertain significance (Nov 11, 2024)
2-67399586-G-A		not specified	Uncertain significance (Sep 27, 2022)
2-67399593-G-C		not specified	Uncertain significance (Jun 17, 2024)
2-67399603-A-G		not specified	Uncertain significance (Dec 16, 2023)
2-67402886-A-C		not specified	Uncertain significance (Jan 31, 2024)
2-67402895-A-T		not specified	Uncertain significance (Feb 27, 2023)
2-67402901-A-C		not specified	Uncertain significance (Apr 05, 2023)
2-67402907-G-A		not specified	Uncertain significance (Nov 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ETAA1	protein_coding	protein_coding	ENST00000272342	6	13227

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00780	0.992	125693	0	17	125710	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.244	439	454	0.968	0.0000205	6151
Missense in Polyphen		89	106.95	0.83214		1652
Synonymous	0.812	149	162	0.919	0.00000776	1680
Loss of Function	3.68	10	32.7	0.306	0.00000148	459

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000448	0.000435
Finnish	0.0000940	0.0000924
European (Non-Finnish)	0.0000531	0.0000528
Middle Eastern	0.000448	0.000435
South Asian	0.0000330	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Replication stress response protein that accumulates at DNA damage sites and promotes replication fork progression and integrity (PubMed:27601467, PubMed:27723720, PubMed:27723717). Recruited to stalled replication forks via interaction with the RPA complex and directly stimulates ATR kinase activity independently of TOPBP1 (PubMed:27723720, PubMed:27723717). Probably only regulates a subset of ATR targets (PubMed:27723720, PubMed:27723717). {ECO:0000269|PubMed:27601467, ECO:0000269|PubMed:27723717, ECO:0000269|PubMed:27723720}.

Recessive Scores

• pRec: 0.0788

Intolerance Scores

• loftool: 0.844
• rvis_EVS: 1.49
• rvis_percentile_EVS: 95.36

Haploinsufficiency Scores

• pHI: 0.0514
• hipred: N
• hipred_score: 0.273
• ghis: 0.443

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0338

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Etaa1

Gene ontology

• Biological process: DNA repair;cellular response to DNA damage stimulus;replication fork processing;positive regulation of protein serine/threonine kinase activity;regulation of DNA damage checkpoint
• Cellular component: nuclear replication fork
• Molecular function: protein binding;protein serine/threonine kinase activator activity