XRRA1

X-ray radiation resistance associated 1

Basic information

Region (hg38): 11:74807738-74949200

Links

ENSG00000166435 ∙ NCBI:143570 ∙ OMIM:609788 ∙ HGNC:18868 ∙ Uniprot:Q6P2D8 ∙ 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 XRRA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the XRRA1 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			49	5		54
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3			3
Total	0	0	52	7	0

Variants in XRRA1

This is a list of pathogenic ClinVar variants found in the XRRA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-74810328-C-T		not specified	Uncertain significance (May 01, 2022)
11-74810329-G-A		not specified	Likely benign (Feb 28, 2024)
11-74817603-C-T		not specified	Uncertain significance (Apr 28, 2022)
11-74817663-G-T		not specified	Uncertain significance (Mar 07, 2023)
11-74834752-G-A		not specified	Uncertain significance (Jul 06, 2021)
11-74835609-C-T		not specified	Uncertain significance (Dec 21, 2022)
11-74835615-G-A		not specified	Uncertain significance (Dec 08, 2023)
11-74835615-G-T		not specified	Uncertain significance (Aug 23, 2021)
11-74835624-C-A		not specified	Uncertain significance (Nov 07, 2023)
11-74835645-C-T		not specified	Uncertain significance (Jun 24, 2022)
11-74835826-A-G		not specified	Uncertain significance (Oct 05, 2023)
11-74835837-C-T		not specified	Uncertain significance (Mar 28, 2024)
11-74835895-T-C		not specified	Uncertain significance (Nov 06, 2023)
11-74835909-C-A		not specified	Uncertain significance (Jun 02, 2023)
11-74835963-T-G		not specified	Uncertain significance (Apr 15, 2024)
11-74836003-A-G		not specified	Uncertain significance (Sep 01, 2021)
11-74836039-C-T		not specified	Uncertain significance (Oct 02, 2023)
11-74836207-A-G		not specified	Likely benign (Jun 22, 2021)
11-74836228-C-G		not specified	Uncertain significance (May 23, 2023)
11-74836233-G-A		not specified	Uncertain significance (Jun 11, 2021)
11-74836425-G-A		not specified	Uncertain significance (Nov 09, 2022)
11-74836458-C-T		not specified	Uncertain significance (Feb 28, 2023)
11-74836510-C-G		not specified	Uncertain significance (Aug 08, 2022)
11-74836536-G-A		not specified	Uncertain significance (Feb 27, 2023)
11-74836678-G-A		not specified	Uncertain significance (Oct 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
XRRA1	protein_coding	protein_coding	ENST00000340360	17	141462

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.37e-9	0.995	124512	2	223	124737	0.000902

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0319	441	439	1.00	0.0000250	5111
Missense in Polyphen		143	138.79	1.0303		1742
Synonymous	1.79	147	177	0.829	0.00000982	1586
Loss of Function	2.58	19	35.6	0.534	0.00000175	458

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000419	0.000419
Ashkenazi Jewish	0.0120	0.0119
East Asian	0.000560	0.000556
Finnish	0.00	0.00
European (Non-Finnish)	0.000449	0.000442
Middle Eastern	0.000560	0.000556
South Asian	0.000919	0.000850
Other	0.00132	0.00132

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in the response of cells to X-ray radiation. {ECO:0000269|PubMed:12908878}.

Recessive Scores

• pRec: 0.0771

Intolerance Scores

• loftool: 0.965
• rvis_EVS: 1.72
• rvis_percentile_EVS: 96.49

Haploinsufficiency Scores

• pHI: 0.0720
• hipred: N
• hipred_score: 0.273
• ghis: 0.428

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0195

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Xrra1

Gene ontology

• Biological process: response to X-ray
• Cellular component: nucleus;nucleoplasm;cytoplasm;nuclear body
• Molecular function: molecular_function