RPA2

replication protein A2, the group of Nucleotide excision repair

Basic information

Region (hg38): 1:27891523-27914746

Links

ENSG00000117748 ∙ NCBI:6118 ∙ OMIM:179836 ∙ HGNC:10290 ∙ Uniprot:P15927 ∙ 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 RPA2 gene.

• Inborn genetic diseases (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPA2 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			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	0

Variants in RPA2

This is a list of pathogenic ClinVar variants found in the RPA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-27892171-C-T		not specified	Uncertain significance (Dec 07, 2021)
1-27892190-G-T		not specified	Uncertain significance (Oct 10, 2023)
1-27894054-T-C		not specified	Uncertain significance (Mar 22, 2023)
1-27894055-C-T		not specified	Uncertain significance (Nov 07, 2023)
1-27894088-C-A		not specified	Uncertain significance (Feb 05, 2024)
1-27894376-T-C		not specified	Uncertain significance (Jul 12, 2023)
1-27897039-T-C		not specified	Uncertain significance (May 27, 2022)
1-27897105-A-C		not specified	Uncertain significance (Nov 18, 2022)
1-27897688-G-A		not specified	Uncertain significance (Nov 02, 2023)
1-27907224-A-C		not specified	Uncertain significance (May 26, 2022)
1-27914065-A-G		not specified	Uncertain significance (Apr 18, 2023)
1-27914142-G-A		not specified	Uncertain significance (Sep 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPA2	protein_coding	protein_coding	ENST00000373912	9	23223

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.505	0.495	125737	0	6	125743	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.774	119	145	0.819	0.00000653	1788
Missense in Polyphen		31	47.007	0.65947		617
Synonymous	0.0660	51	51.6	0.988	0.00000238	509
Loss of Function	2.85	3	14.8	0.202	7.13e-7	176

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000544	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: As part of the heterotrimeric replication protein A complex (RPA/RP-A), binds and stabilizes single-stranded DNA intermediates, that form during DNA replication or upon DNA stress. It prevents their reannealing and in parallel, recruits and activates different proteins and complexes involved in DNA metabolism. Thereby, it plays an essential role both in DNA replication and the cellular response to DNA damage. In the cellular response to DNA damage, the RPA complex controls DNA repair and DNA damage checkpoint activation. Through recruitment of ATRIP activates the ATR kinase a master regulator of the DNA damage response. It is required for the recruitment of the DNA double-strand break repair factors RAD51 and RAD52 to chromatin in response to DNA damage. Also recruits to sites of DNA damage proteins like XPA and XPG that are involved in nucleotide excision repair and is required for this mechanism of DNA repair. Plays also a role in base excision repair (BER) probably through interaction with UNG. Also recruits SMARCAL1/HARP, which is involved in replication fork restart, to sites of DNA damage. May also play a role in telomere maintenance. {ECO:0000269|PubMed:15205463, ECO:0000269|PubMed:17765923, ECO:0000269|PubMed:17959650, ECO:0000269|PubMed:19116208, ECO:0000269|PubMed:20154705, ECO:0000269|PubMed:21504906, ECO:0000269|PubMed:2406247, ECO:0000269|PubMed:24332808, ECO:0000269|PubMed:7697716, ECO:0000269|PubMed:7700386, ECO:0000269|PubMed:8702565, ECO:0000269|PubMed:9430682, ECO:0000269|PubMed:9765279}.
• Pathway: Fanconi anemia pathway - Homo sapiens (human);Nucleotide excision repair - Homo sapiens (human);Mismatch repair - Homo sapiens (human);DNA replication - Homo sapiens (human);Homologous recombination - Homo sapiens (human);miRNA Regulation of DNA Damage Response;Retinoblastoma (RB) in Cancer;G1 to S cell cycle control;DNA Replication;DNA Damage Response;Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta);Mismatch Repair;HDR through Single Strand Annealing (SSA);HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA);Fanconi Anemia Pathway;DNA Repair;Gene expression (Transcription);DNA Double-Strand Break Repair;HSF1 activation;Generic Transcription Pathway;Regulation of HSF1-mediated heat shock response;Homology Directed Repair;Cellular responses to stress;RNA Polymerase II Transcription;G2/M DNA damage checkpoint;Activation of ATR in response to replication stress;G2/M Checkpoints;Cell Cycle Checkpoints;Activation of the pre-replicative complex;Mitotic G1-G1/S phases;DNA Replication;Removal of the Flap Intermediate;Processive synthesis on the lagging strand;Lagging Strand Synthesis;DNA strand elongation;Synthesis of DNA;S Phase;PCNA-Dependent Long Patch Base Excision Repair;Resolution of AP sites via the multiple-nucleotide patch replacement pathway;Resolution of Abasic Sites (AP sites);Base Excision Repair;Cellular responses to external stimuli;Removal of the Flap Intermediate from the C-strand;Processive synthesis on the C-strand of the telomere;Telomere C-strand (Lagging Strand) Synthesis;Extension of Telomeres;Telomere Maintenance;Chromosome Maintenance;Fanconi anemia pathway;Cellular response to heat stress;G1/S Transition;Regulation of TP53 Activity through Phosphorylation;Regulation of TP53 Activity;Transcriptional Regulation by TP53;Recognition of DNA damage by PCNA-containing replication complex;Translesion synthesis by REV1;Translesion Synthesis by POLH;Translesion synthesis by POLK;DNA Replication Pre-Initiation;M/G1 Transition;Translesion synthesis by POLI;Termination of translesion DNA synthesis;Translesion synthesis by Y family DNA polymerases bypasses lesions on DNA template;DNA Damage Bypass;Cell Cycle;Formation of Incision Complex in GG-NER;Dual Incision in GG-NER;Gap-filling DNA repair synthesis and ligation in GG-NER;Global Genome Nucleotide Excision Repair (GG-NER);Cell Cycle, Mitotic;Processing of DNA double-strand break ends;ATR signaling pathway;Dual incision in TC-NER;Presynaptic phase of homologous DNA pairing and strand exchange;Homologous DNA Pairing and Strand Exchange;Gap-filling DNA repair synthesis and ligation in TC-NER;Transcription-Coupled Nucleotide Excision Repair (TC-NER);Nucleotide Excision Repair;Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha);HDR through Homologous Recombination (HRR) (Consensus)

Recessive Scores

• pRec: 0.391

Intolerance Scores

• loftool: 0.550
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.06

Haploinsufficiency Scores

• pHI: 0.889
• hipred: Y
• hipred_score: 0.712
• ghis: 0.533

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.984

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rpa2

Gene ontology

• Biological process: G1/S transition of mitotic cell cycle;telomere maintenance via recombination;telomere maintenance;double-strand break repair via homologous recombination;DNA replication;DNA topological change;DNA unwinding involved in DNA replication;transcription-coupled nucleotide-excision repair;base-excision repair;nucleotide-excision repair;nucleotide-excision repair, preincision complex stabilization;nucleotide-excision repair, preincision complex assembly;nucleotide-excision repair, DNA incision, 5'-to lesion;nucleotide-excision repair, DNA gap filling;mismatch repair;mitotic recombination;telomere maintenance via telomerase;reciprocal meiotic recombination;regulation of double-strand break repair via homologous recombination;translesion synthesis;heteroduplex formation;mitotic G1 DNA damage checkpoint;telomere maintenance via semi-conservative replication;nucleotide-excision repair, DNA incision;protein localization to chromosome;interstrand cross-link repair;error-prone translesion synthesis;DNA damage response, detection of DNA damage;positive regulation of helicase activity;error-free translesion synthesis;regulation of cellular response to heat;regulation of DNA damage checkpoint
• Cellular component: chromosome, telomeric region;nuclear chromosome, telomeric region;chromatin;condensed nuclear chromosome;nucleus;nucleoplasm;DNA replication factor A complex;nuclear body;PML body;site of double-strand break
• Molecular function: damaged DNA binding;double-stranded DNA binding;single-stranded DNA binding;protein binding;enzyme binding;protein phosphatase binding;ubiquitin protein ligase binding;sequence-specific DNA binding;protein N-terminus binding;G-rich strand telomeric DNA binding