RFC2

replication factor C subunit 2, the group of AAA ATPases

Basic information

Region (hg38): 7:74231499-74254458

Links

ENSG00000049541 ∙ NCBI:5982 ∙ OMIM:600404 ∙ HGNC:9970 ∙ Uniprot:P35250 ∙ 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 RFC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RFC2 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				9	4	13
missense			23	3	1	27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	3	4
non coding				1		1
Total	0	0	23	13	5

Variants in RFC2

This is a list of pathogenic ClinVar variants found in the RFC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-74232119-G-A			Likely benign (Dec 31, 2019)
7-74232130-C-A		not specified	Uncertain significance (Jan 16, 2025)
7-74232139-C-T			Likely benign (Dec 31, 2019)
7-74232190-T-C		not specified	Uncertain significance (Nov 28, 2024)
7-74232191-A-C		not specified	Uncertain significance (Oct 26, 2022)
7-74232198-T-C		not specified	Uncertain significance (Aug 26, 2022)
7-74235617-T-A		not specified	Uncertain significance (Aug 13, 2021)
7-74237374-G-A			Likely benign (Dec 31, 2019)
7-74237378-A-G		not specified	Uncertain significance (Jun 17, 2024)
7-74237422-T-G			Likely benign (Nov 01, 2022)
7-74238915-G-A			Benign (Dec 31, 2019)
7-74238924-T-A		not specified	Uncertain significance (Aug 31, 2023)
7-74238987-G-A			Likely benign (Sep 01, 2024)
7-74239960-G-A		not specified	Uncertain significance (Dec 21, 2023)
7-74239985-C-T		not specified	Uncertain significance (Aug 30, 2021)
7-74239997-G-A		not specified	Uncertain significance (Jan 29, 2025)
7-74240012-C-T			Benign (Dec 31, 2019)
7-74240014-A-G		not specified	Uncertain significance (Jul 27, 2021)
7-74240030-T-G			Benign (Dec 31, 2019)
7-74240045-C-T			Uncertain significance (Feb 01, 2023)
7-74240046-G-A			Likely benign (May 31, 2018)
7-74240059-G-A		not specified	Uncertain significance (Feb 07, 2025)
7-74240066-G-A		not specified	Uncertain significance (Jan 23, 2024)
7-74243232-G-A		not specified	Uncertain significance (Jul 14, 2024)
7-74243237-G-A			Likely benign (Apr 07, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RFC2	protein_coding	protein_coding	ENST00000055077	11	22946

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000221	0.906	125692	0	56	125748	0.000223

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.15	160	207	0.774	0.0000112	2330
Missense in Polyphen		31	60.551	0.51196		657
Synonymous	-0.461	88	82.7	1.06	0.00000515	679
Loss of Function	1.64	12	19.9	0.603	9.96e-7	229

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000366	0.000366
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000230	0.000229
Middle Eastern	0.000109	0.000109
South Asian	0.000509	0.000490
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: The elongation of primed DNA templates by DNA polymerase delta and epsilon requires the action of the accessory proteins proliferating cell nuclear antigen (PCNA) and activator 1. This subunit binds ATP (By similarity). {ECO:0000250}.
• Disease: DISEASE: Note=RFC2 is located in the Williams-Beuren syndrome (WBS) critical region. WBS results from a hemizygous deletion of several genes on chromosome 7q11.23, thought to arise as a consequence of unequal crossing over between highly homologous low-copy repeat sequences flanking the deleted region (PubMed:11003705). {ECO:0000269|PubMed:11003705}.
• Pathway: Nucleotide excision repair - Homo sapiens (human);Mismatch repair - Homo sapiens (human);DNA replication - Homo sapiens (human);DNA Replication;HDR through Single Strand Annealing (SSA);HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA);DNA Repair;Gene expression (Transcription);DNA Double-Strand Break Repair;Generic Transcription Pathway;Homology Directed Repair;Polymerase switching on the C-strand of the telomere;RNA Polymerase II Transcription;G2/M DNA damage checkpoint;Activation of ATR in response to replication stress;G2/M Checkpoints;Cell Cycle Checkpoints;DNA Replication;Polymerase switching;Leading Strand Synthesis;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;Telomere C-strand (Lagging Strand) Synthesis;Extension of Telomeres;Telomere Maintenance;Chromosome Maintenance;Fanconi anemia pathway;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;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;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;HDR through Homologous Recombination (HRR) (Consensus)

Recessive Scores

• pRec: 0.339

Intolerance Scores

• loftool: 0.510
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.54

Haploinsufficiency Scores

• pHI: 0.809
• hipred: Y
• hipred_score: 0.617
• ghis: 0.574

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.936

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rfc2

Gene ontology

• Biological process: DNA replication;DNA-dependent DNA replication;transcription-coupled nucleotide-excision repair;nucleotide-excision repair, DNA incision, 5'-to lesion;nucleotide-excision repair, DNA gap filling;translesion synthesis;telomere maintenance via semi-conservative replication;nucleotide-excision repair, DNA incision;error-prone translesion synthesis;DNA damage response, detection of DNA damage;error-free translesion synthesis;positive regulation of DNA-directed DNA polymerase activity
• Cellular component: nucleus;nucleoplasm;DNA replication factor C complex;Ctf18 RFC-like complex
• Molecular function: DNA clamp loader activity;protein binding;ATP binding;enzyme binding;single-stranded DNA-dependent ATPase activity