RFC3
Basic information
Region (hg38): 13:33818068-33966558
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (9 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.
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 | 9 | |||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region ? | 0 | |||||
non coding ? | 0 | |||||
Total | 0 | 0 | 9 | 0 | 0 |
Variants in RFC3
This is a list of pathogenic ClinVar variants found in the RFC3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
13-33818184-C-G | not specified | Uncertain significance (Dec 20, 2023) | ||
13-33818224-C-G | not specified | Uncertain significance (Mar 07, 2024) | ||
13-33818231-A-G | not specified | Uncertain significance (Aug 31, 2022) | ||
13-33821136-A-G | not specified | Uncertain significance (Jan 29, 2024) | ||
13-33823948-C-T | not specified | Uncertain significance (Aug 10, 2021) | ||
13-33829848-C-T | not specified | Uncertain significance (Jul 09, 2021) | ||
13-33829986-C-T | not specified | Uncertain significance (Aug 22, 2023) | ||
13-33830776-C-G | not specified | Uncertain significance (Dec 19, 2022) | ||
13-33835171-T-A | not specified | Uncertain significance (Oct 26, 2021) | ||
13-33835192-G-T | not specified | Uncertain significance (Feb 12, 2024) | ||
13-33836110-C-T | not specified | Uncertain significance (Nov 09, 2023) | ||
13-33836185-C-T | not specified | Uncertain significance (Oct 22, 2021) | ||
13-33836252-A-G | not specified | Uncertain significance (Dec 20, 2021) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
RFC3 | protein_coding | protein_coding | ENST00000380071 | 9 | 148510 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00000958 | 0.939 | 125700 | 0 | 48 | 125748 | 0.000191 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.128 | 196 | 191 | 1.03 | 0.00000946 | 2324 |
Missense in Polyphen | 71 | 73.433 | 0.96687 | 870 | ||
Synonymous | -0.135 | 66 | 64.6 | 1.02 | 0.00000316 | 663 |
Loss of Function | 1.75 | 11 | 19.3 | 0.569 | 9.80e-7 | 243 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000314 | 0.000314 |
Ashkenazi Jewish | 0.000101 | 0.0000992 |
East Asian | 0.0000544 | 0.0000544 |
Finnish | 0.000140 | 0.000139 |
European (Non-Finnish) | 0.000278 | 0.000273 |
Middle Eastern | 0.0000544 | 0.0000544 |
South Asian | 0.000138 | 0.000131 |
Other | 0.000175 | 0.000163 |
dbNSFP
Source:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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