RADX

RPA1 related single stranded DNA binding protein, X-linked, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): X:106611930-106679439

Previous symbols: [ "CXorf57" ]

Links

ENSG00000147231 ∙ NCBI:55086 ∙ ∙ HGNC:25486 ∙ Uniprot:Q6NSI4 ∙ 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 RADX gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RADX 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	1	4
missense			1	2	1	4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	1	5	2

Variants in RADX

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

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

Position	Type	Phenotype	Significance	ClinVar
X-106612538-T-C			Benign (Dec 11, 2018)
X-106632617-T-C			Likely benign (May 01, 2023)
X-106632644-A-C			Benign (Dec 20, 2017)
X-106633242-T-C			Likely benign (Mar 01, 2022)
X-106640646-A-G		not specified	Uncertain significance (Oct 05, 2021)
X-106640659-T-C			Likely benign (Jan 01, 2023)
X-106640716-T-A			Likely benign (Feb 01, 2023)
X-106662135-G-A			Likely benign (Apr 01, 2023)
X-106669304-G-A			Likely benign (Feb 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RADX	protein_coding	protein_coding	ENST00000372548	14	67513

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000271	0.999	125724	7	14	125745	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.95	216	313	0.690	0.0000227	5605
Missense in Polyphen		42	84.421	0.49751		1695
Synonymous	-0.209	118	115	1.02	0.00000840	1635
Loss of Function	2.99	11	28.1	0.392	0.00000210	506

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000227	0.000197
Ashkenazi Jewish	0.00	0.00
East Asian	0.000153	0.000109
Finnish	0.000126	0.0000924
European (Non-Finnish)	0.000151	0.000105
Middle Eastern	0.000153	0.000109
South Asian	0.0000524	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Single-stranded DNA-binding protein recruited to replication forks to maintain genome stability (PubMed:28735897). Prevents fork collapse by antagonizing the accumulation of RAD51 at forks to ensure the proper balance of fork remodeling and protection without interfering with the capacity of cells to complete homologous recombination of double-strand breaks (PubMed:28735897). {ECO:0000269|PubMed:28735897}.

Intolerance Scores

• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.73

Haploinsufficiency Scores

• pHI: 0.570
• hipred: Y
• hipred_score: 0.571
• ghis: 0.560

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: D330045A20Rik

Gene ontology

• Biological process: negative regulation of double-strand break repair via homologous recombination
• Cellular component: replication fork
• Molecular function: single-stranded DNA binding;RNA binding;protein binding