RPAIN

RPA interacting protein

Basic information

Region (hg38): 17:5419641-5432877

Links

ENSG00000129197NCBI:84268OMIM:617299HGNC:28641Uniprot:Q86UA6AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPAIN gene.

  • not_specified (31 variants)
  • not_provided (1 variants)
  • See_cases (1 variants)

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. These statistics are base on transcript: NM_001033002.4. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
missense
26
clinvar
1
clinvar
27
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 26 1 1
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPAINprotein_codingprotein_codingENST00000405578 613236
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
5.57e-110.01721256950531257480.000211
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.1391211250.9650.000006121513
Missense in Polyphen4141.4080.99014480
Synonymous-0.7065346.91.130.00000229427
Loss of Function-0.8351411.01.274.67e-7134

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002420.000242
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.00004680.0000462
European (Non-Finnish)0.0003620.000360
Middle Eastern0.00005440.0000544
South Asian0.0001310.000131
Other0.0001640.000163

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rpain
Phenotype

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