RPAIN

RPA interacting protein

Basic information

Region (hg38): 17:5419640-5432877

Links

ENSG00000129197 ∙ NCBI:84268 ∙ OMIM:617299 ∙ HGNC:28641 ∙ Uniprot:Q86UA6 ∙ 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 RPAIN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPAIN 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						0
missense			8		1	9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			2	1		3
non coding					1	1
Total	0	0	8	0	2

Variants in RPAIN

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

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

Position	Type	Phenotype	Significance	ClinVar
17-5420236-G-C		not specified	Uncertain significance (Oct 14, 2023)
17-5420238-C-T		not specified	Uncertain significance (Apr 20, 2024)
17-5421435-C-T		not specified	Uncertain significance (Apr 29, 2024)
17-5422793-G-A		not specified	Uncertain significance (Mar 16, 2024)
17-5426079-C-A		not specified	Uncertain significance (Apr 15, 2022)
17-5426255-A-G			Benign (Aug 04, 2017)
17-5426280-G-A		not specified	Uncertain significance (May 23, 2024)
17-5428065-T-C		See cases	Uncertain significance (-)
17-5428110-G-C		not specified	Uncertain significance (Oct 03, 2022)
17-5428130-C-A		not specified	Uncertain significance (Mar 01, 2023)
17-5428147-A-G		not specified	Uncertain significance (Jun 09, 2022)
17-5428168-C-T		not specified	Uncertain significance (Jul 14, 2021)
17-5428179-G-A		not specified	Uncertain significance (Jan 02, 2024)
17-5428201-T-G		not specified	Uncertain significance (Jun 29, 2023)
17-5428215-A-G		not specified	Uncertain significance (Oct 02, 2023)
17-5428217-C-T		not specified	Likely benign (Sep 14, 2023)
17-5432868-A-G			Benign (May 10, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPAIN	protein_coding	protein_coding	ENST00000405578	6	13236

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.57e-11	0.0172	125695	0	53	125748	0.000211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.139	121	125	0.965	0.00000612	1513
Missense in Polyphen		41	41.408	0.99014		480
Synonymous	-0.706	53	46.9	1.13	0.00000229	427
Loss of Function	-0.835	14	11.0	1.27	4.67e-7	134

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000242	0.000242
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000468	0.0000462
European (Non-Finnish)	0.000362	0.000360
Middle Eastern	0.0000544	0.0000544
South Asian	0.000131	0.000131
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates the import of RPA complex into the nucleus, possibly via some interaction with importin beta. Isoform 2 is sumoylated and mediates the localization of RPA complex into the PML body of the nucleus, thereby participating in RPA function in DNA metabolism. {ECO:0000269|PubMed:16135809}.

Intolerance Scores

• loftool: 0.968
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.51

Haploinsufficiency Scores

• pHI: 0.198
• hipred: N
• hipred_score: 0.170
• ghis: 0.544

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0964

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rpain

Gene ontology

• Biological process: DNA-dependent DNA replication;DNA repair;DNA recombination;protein import into nucleus
• Cellular component: fibrillar center;nucleus;cytoplasm;PML body
• Molecular function: protein-containing complex binding;metal ion binding