GeneBe

RFC3

replication factor C subunit 3, the group of AAA ATPases

Basic information

Region (hg38): 13:33818069-33966558

Links

ENSG00000133119 ∙ NCBI:5983 ∙ OMIM:600405 ∙ HGNC:9971 ∙ Uniprot:P40938 ∙ 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 RFC3 gene.

  • not_specified (39 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RFC3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002915.4. 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
0
missense
39
clinvar
 39
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 39 0 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RFC3protein_codingprotein_codingENST00000380071 9148510
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.000009580.9391257000481257480.000191
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.1281961911.030.000009462324
Missense in Polyphen7173.4330.96687870
Synonymous-0.1356664.61.020.00000316663
Loss of Function1.751119.30.5699.80e-7243

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003140.000314
Ashkenazi Jewish0.0001010.0000992
East Asian0.00005440.0000544
Finnish0.0001400.000139
European (Non-Finnish)0.0002780.000273
Middle Eastern0.00005440.0000544
South Asian0.0001380.000131
Other0.0001750.000163

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.;
Pathway
Nucleotide excision repair - Homo sapiens (human);Mismatch repair - Homo sapiens (human);DNA replication - Homo sapiens (human);Gastric Cancer Network 2;Retinoblastoma (RB) in Cancer;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
0.277

Intolerance Scores

loftool
0.862
rvis_EVS
-0.56
rvis_percentile_EVS
19.31

Haploinsufficiency Scores

pHI
0.973
hipred
Y
hipred_score
0.718
ghis
0.745

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.972

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rfc3
Phenotype

Gene ontology

Biological process
DNA synthesis involved in DNA repair;DNA replication;DNA-dependent DNA replication;DNA strand elongation involved in 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;response to organophosphorus;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 binding;DNA clamp loader activity;protein binding;ATPase activity;single-stranded DNA-dependent ATPase activity