RPA4
Basic information
Region (hg38): X:96883908-96885467
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (39 variants)
- not_provided (3 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPA4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000013347.4. 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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 35 | 40 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 35 | 6 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RPA4 | protein_coding | protein_coding | ENST00000373040 | 1 | 1540 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.251 | 107 | 115 | 0.934 | 0.00000952 | 1730 |
| Missense in Polyphen | 24 | 22.638 | 1.0601 | 417 | ||
| Synonymous | 1.51 | 34 | 47.2 | 0.720 | 0.00000432 | 520 |
| Loss of Function |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | ||
| East Asian | ||
| Finnish | ||
| European (Non-Finnish) | ||
| Middle Eastern | ||
| South Asian | ||
| Other |
dbNSFP
Source:
- Function
- FUNCTION: As part of the alternative replication protein A complex, aRPA, binds single-stranded DNA and probably plays a role in DNA repair. Compared to the RPA2-containing, canonical RPA complex, may not support chromosomal DNA replication and cell cycle progression through S-phase. The aRPA may not promote efficient priming by DNA polymerase alpha but could support DNA polymerase delta synthesis in the presence of PCNA and replication factor C (RFC), the dual incision/excision reaction of nucleotide excision repair and RAD51-dependent strand exchange. {ECO:0000269|PubMed:19116208, ECO:0000269|PubMed:19942684, ECO:0000269|PubMed:19996105, ECO:0000269|PubMed:20545304}.;
- 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);DNA Replication;Activation of the pre-replicative complex;Mitotic G1-G1/S phases;DNA Replication;G1/S Transition;DNA Replication Pre-Initiation;M/G1 Transition;Cell Cycle;Cell Cycle, Mitotic
(Consensus)
Intolerance Scores
- loftool
- 0.539
- rvis_EVS
- -0.01
- rvis_percentile_EVS
- 53.19
Haploinsufficiency Scores
- pHI
- 0.172
- hipred
- N
- hipred_score
- 0.329
- ghis
- 0.394
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.914
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Gene ontology
- Biological process
- DNA damage checkpoint;G1/S transition of mitotic cell cycle;telomere maintenance via recombination;double-strand break repair via homologous recombination;DNA replication;DNA topological change;DNA unwinding involved in DNA replication;DNA replication initiation;base-excision repair;nucleotide-excision repair;mismatch repair;mitotic recombination;telomere maintenance via telomerase;reciprocal meiotic recombination;heteroduplex formation;nuclear DNA replication;positive regulation of helicase activity;regulation of DNA damage checkpoint
- Cellular component
- chromosome, telomeric region;chromatin;condensed nuclear chromosome;nucleus;nucleoplasm;DNA replication factor A complex;site of double-strand break
- Molecular function
- damaged DNA binding;double-stranded DNA binding;single-stranded DNA binding;protein binding;sequence-specific DNA binding;G-rich strand telomeric DNA binding