RFC4
replication factor C subunit 4, the group of AAA ATPases
Basic information
Region (hg38): 3:186789880-186807058
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RFC4 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 | 20 | 21 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 20 | 1 | 1 |
Variants in RFC4
This is a list of pathogenic ClinVar variants found in the RFC4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 3-186789995-TCA-T | MORIMOTO-RYU-MALICDAN NEUROMUSCULAR SYNDROME | Pathogenic (Nov 13, 2024) | ||
| 3-186790031-C-T | MORIMOTO-RYU-MALICDAN NEUROMUSCULAR SYNDROME | Pathogenic (Nov 13, 2024) | ||
| 3-186790036-G-A | not specified | Uncertain significance (Jun 04, 2024) | ||
| 3-186790133-C-T | Benign (Oct 30, 2018) | |||
| 3-186790139-T-TA | MORIMOTO-RYU-MALICDAN NEUROMUSCULAR SYNDROME | Pathogenic (Nov 13, 2024) | ||
| 3-186790155-G-GTGA | MORIMOTO-RYU-MALICDAN NEUROMUSCULAR SYNDROME | Pathogenic (Nov 13, 2024) | ||
| 3-186790159-T-C | not specified | Uncertain significance (Feb 28, 2024) | ||
| 3-186790180-A-C | not specified | Uncertain significance (Apr 01, 2024) | ||
| 3-186790187-ATTTT-A | MORIMOTO-RYU-MALICDAN NEUROMUSCULAR SYNDROME | Pathogenic (Nov 13, 2024) | ||
| 3-186790213-G-C | not specified | Uncertain significance (Oct 12, 2021) | ||
| 3-186790215-T-A | not specified | Uncertain significance (Dec 07, 2021) | ||
| 3-186790221-A-T | not specified | Uncertain significance (Feb 17, 2022) | ||
| 3-186790228-TTGC-T | MORIMOTO-RYU-MALICDAN NEUROMUSCULAR SYNDROME | Pathogenic (Nov 13, 2024) | ||
| 3-186790241-C-G | not specified | Uncertain significance (Jul 14, 2022) | ||
| 3-186790245-T-C | not specified | Uncertain significance (Feb 13, 2024) | ||
| 3-186790343-G-C | not specified | Uncertain significance (May 07, 2024) | ||
| 3-186790349-C-G | not specified | Uncertain significance (Jan 08, 2024) | ||
| 3-186790363-T-C | not specified | Uncertain significance (Mar 19, 2024) | ||
| 3-186790367-A-G | MORIMOTO-RYU-MALICDAN NEUROMUSCULAR SYNDROME | Pathogenic (Nov 13, 2024) | ||
| 3-186790373-C-T | not specified | Uncertain significance (Apr 16, 2024) | ||
| 3-186790381-C-T | not specified | Uncertain significance (Mar 16, 2022) | ||
| 3-186790381-CCAT-C | MORIMOTO-RYU-MALICDAN NEUROMUSCULAR SYNDROME | Pathogenic (Nov 13, 2024) | ||
| 3-186790396-G-A | not specified | Uncertain significance (Nov 30, 2021) | ||
| 3-186790403-T-C | not specified | Uncertain significance (Jan 04, 2022) | ||
| 3-186791727-C-G | not specified | Uncertain significance (Nov 14, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RFC4 | protein_coding | protein_coding | ENST00000392481 | 10 | 17179 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 4.50e-7 | 0.957 | 125613 | 0 | 135 | 125748 | 0.000537 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.288 | 211 | 200 | 1.06 | 0.0000107 | 2338 |
| Missense in Polyphen | 56 | 78.881 | 0.70993 | 915 | ||
| Synonymous | 0.276 | 68 | 71.0 | 0.958 | 0.00000388 | 713 |
| Loss of Function | 1.94 | 14 | 24.3 | 0.576 | 0.00000166 | 258 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00146 | 0.00146 |
| Ashkenazi Jewish | 0.000397 | 0.000397 |
| East Asian | 0.000382 | 0.000381 |
| Finnish | 0.000647 | 0.000647 |
| European (Non-Finnish) | 0.000440 | 0.000440 |
| Middle Eastern | 0.000382 | 0.000381 |
| South Asian | 0.000687 | 0.000686 |
| Other | 0.000327 | 0.000326 |
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. This subunit may be involved in the elongation of the multiprimed DNA template.;
- 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
- 0.146
Intolerance Scores
- loftool
- 0.975
- rvis_EVS
- -0.67
- rvis_percentile_EVS
- 15.76
Haploinsufficiency Scores
- pHI
- 0.997
- hipred
- Y
- hipred_score
- 0.723
- ghis
- 0.722
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.965
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rfc4
- Phenotype
Zebrafish Information Network
- Gene name
- rfc4
- Affected structure
- head
- Phenotype tag
- abnormal
- Phenotype quality
- pointed
Gene ontology
- Biological process
- 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;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;Elg1 RFC-like complex
- Molecular function
- DNA clamp loader activity;protein binding;ATP binding;enzyme binding;single-stranded DNA-dependent ATPase activity