RAD51AP1
protein-codingRAD51 associated protein 1
Gene summary
Enables DNA binding activity and RNA binding activity. Involved in DNA repair; cellular response to ionizing radiation; and positive regulation of DNA recombination. Located in chromatin and nucleus. Part of protein-containing complex. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~21.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to RAD51AP1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006479.5. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 44 | 4 | 3 | 51 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 45 | 4 | 4 | 53 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_006470.1 | 9 | MANE Select | |
| Ensembl | ENSP00000309479.7 | 9 | MANE Select | |
| RefSeq | NP_001124334.1 | 10 | Standard | |
| RefSeq | NP_001397888.1 | 8 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA)
- DNA Repair
- DNA Double-Strand Break Repair
- Homology Directed Repair
- Homologous DNA Pairing and Strand Exchange
Biological Process
- double-strand break repair via homologous recombination
- DNA repair
- regulation of double-strand break repair via homologous recombination
- interstrand cross-link repair
- cellular response to ionizing radiation
Molecular Function
- double-stranded DNA binding
- single-stranded DNA binding
- RNA binding
- protein binding
Cellular Component
- nuclear chromatin
- nucleus
- nucleoplasm
- protein-containing complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000228843
- Coding exons
- 10
- Length
- 21265
- Individuals with no LoFs
- 125735
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 11
- Defined
- 125747
- p
- 0.0000477
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.469 | 160 | 178 | 0.901 | 0.00000845 | 2321 |
| Missense (PolyPhen) | 34 | 48.878 | 0.69561 | 769 | ||
| Synonymous | 1.14 | 49 | 60.3 | 0.813 | 0.00000286 | 648 |
| Loss of Function | 2.32 | 6 | 16.0 | 0.374 | 6.72e-7 | 236 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0.000088 | 0.000087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00012 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000044 | 0.000044 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May participate in a common DNA damage response pathway associated with the activation of homologous recombination and double-strand break repair. Functionally cooperates with PALB2 in promoting of D-loop formation by RAD51. Binds to single and double stranded DNA, and is capable of aggregating DNA. Also binds RNA. {ECO:0000269|PubMed:20871616, ECO:0000269|PubMed:9396801}.;
Recessive Scores
- pRec
- 0.0852
Intolerance Scores
- LoFtool
- 0.930
- RVIS EVS
- 0.91
- RVIS percentile EVS
- 89.47
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.601
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |