RAD51D
RAD51 paralog D
Basic information
Region (hg38): 17:35092220-35121522
Previous symbols: [ "RAD51L3" ]
Links
Phenotypes
GenCC
Source:
- breast-ovarian cancer, familial, susceptibility to, 4 (Strong), mode of inheritance: AD
- breast-ovarian cancer, familial, susceptibility to, 4 (Strong), mode of inheritance: AD
- hereditary breast ovarian cancer syndrome (Supportive), mode of inheritance: AD
- breast-ovarian cancer, familial, susceptibility to, 4 (Limited), mode of inheritance: AD
- breast-ovarian cancer, familial, susceptibility to, 3 (Definitive), mode of inheritance: AD
- hereditary breast carcinoma (Limited), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Ovarian cancer, familial, susceptibility to | AD | Oncologic | Surveillance (similar to that described for individuals with variants in BRCA1 or BRCA2) related to ovarian cancer may allow early diagnosis and treatment of neoplasms (eg, ovarian tumors), which may reduce morbidity and mortality; Specific, targeted therapies may be available | Oncologic | 21822267; 23300655; 23372765 |
ClinVar
This is a list of variants' phenotypes submitted to
- Breast-ovarian cancer, familial, susceptibility to, 4 (1173 variants)
- Hereditary cancer-predisposing syndrome (1019 variants)
- not provided (309 variants)
- not specified (176 variants)
- Hereditary breast ovarian cancer syndrome (64 variants)
- Breast and/or ovarian cancer (32 variants)
- Malignant tumor of breast (30 variants)
- RAD51D-related condition (10 variants)
- Gastric cancer (8 variants)
- Neoplasm of ovary (7 variants)
- Hereditary cancer (5 variants)
- Ovarian carcinoma (3 variants)
- Breast and Ovarian Cancer Susceptibility (3 variants)
- Deleterious RAD51D Gene Mutation (3 variants)
- Hereditary site-specific ovarian cancer syndrome (2 variants)
- Familial cancer of breast (2 variants)
- Diffuse midline glioma, H3 K27-altered (1 variants)
- Carcinoma of colon (1 variants)
- Lynch syndrome 1 (1 variants)
- Colorectal cancer (1 variants)
- Breast-ovarian cancer, familial, susceptibility to, 3 (1 variants)
- See cases (1 variants)
- Breast carcinoma (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAD51D 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 | 247 | 252 | ||||
| missense | 669 | 673 | ||||
| nonsense | 28 | 14 | 50 | |||
| start loss | 5 | |||||
| frameshift | 56 | 41 | 104 | |||
| inframe indel | 14 | 15 | ||||
| splice donor/acceptor (+/-2bp) | 34 | 46 | ||||
| splice region ? | 1 | 55 | 54 | 1 | 111 | |
| non coding ? | 29 | 185 | 14 | 228 | ||
| Total | 89 | 93 | 740 | 435 | 16 |
Highest pathogenic variant AF is 0.0000263
Variants in RAD51D
This is a list of pathogenic ClinVar variants found in the RAD51D region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RAD51D | protein_coding | protein_coding | ENST00000590016 | 10 | 21731 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.06e-9 | 0.314 | 125695 | 0 | 53 | 125748 | 0.000211 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.112 | 198 | 194 | 1.02 | 0.0000115 | 2194 |
| Missense in Polyphen | 60 | 57.789 | 1.0383 | 708 | ||
| Synonymous | -0.0429 | 81 | 80.5 | 1.01 | 0.00000492 | 755 |
| Loss of Function | 0.820 | 16 | 20.0 | 0.802 | 0.00000123 | 199 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000271 | 0.000271 |
| Ashkenazi Jewish | 0.000701 | 0.000695 |
| East Asian | 0.000870 | 0.000870 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000168 | 0.000149 |
| Middle Eastern | 0.000870 | 0.000870 |
| South Asian | 0.000196 | 0.000196 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in the homologous recombination repair (HRR) pathway of double-stranded DNA breaks arising during DNA replication or induced by DNA-damaging agents. Bind to single- stranded DNA (ssDNA) and has DNA-dependent ATPase activity. Part of the Rad21 paralog protein complex BCDX2 which acts in the BRCA1-BRCA2-dependent HR pathway. Upon DNA damage, BCDX2 acts downstream of BRCA2 recruitment and upstream of RAD51 recruitment. BCDX2 binds predominantly to the intersection of the four duplex arms of the Holliday junction and to junction of replication forks. The BCDX2 complex was originally reported to bind single- stranded DNA, single-stranded gaps in duplex DNA and specifically to nicks in duplex DNA. Involved in telomere maintenance. The BCDX2 subcomplex XRCC2:RAD51D can stimulate Holliday junction resolution by BLM. {ECO:0000269|PubMed:10871607, ECO:0000269|PubMed:11751635, ECO:0000269|PubMed:11834724, ECO:0000269|PubMed:11842113, ECO:0000269|PubMed:12975363, ECO:0000269|PubMed:15109494, ECO:0000269|PubMed:23149936}.;
- Pathway
- Homologous recombination - Homo sapiens (human);TP53 Regulates Transcription of DNA Repair Genes;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;RNA Polymerase II Transcription;TP53 Regulates Transcription of DNA Repair Genes;Transcriptional Regulation by TP53;Presynaptic phase of homologous DNA pairing and strand exchange;Homologous DNA Pairing and Strand Exchange;Resolution of D-loop Structures through Holliday Junction Intermediates;Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA);Resolution of D-Loop Structures;HDR through Homologous Recombination (HRR)
(Consensus)
Intolerance Scores
- loftool
- rvis_EVS
- 0.53
- rvis_percentile_EVS
- 80.96
Haploinsufficiency Scores
- pHI
- 0.458
- hipred
- N
- hipred_score
- 0.133
- ghis
- 0.500
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rad51d
- Phenotype
- growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); embryo phenotype; limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);
Gene ontology
- Biological process
- telomere maintenance;double-strand break repair via homologous recombination;DNA repair;reciprocal meiotic recombination;interstrand cross-link repair;strand invasion;regulation of cell cycle
- Cellular component
- chromosome, telomeric region;nuclear chromosome, telomeric region;nucleus;nucleoplasm;replication fork;cytoplasm;centrosome;Rad51B-Rad51C-Rad51D-XRCC2 complex
- Molecular function
- four-way junction DNA binding;DNA binding;single-stranded DNA binding;protein binding;ATP binding;DNA-dependent ATPase activity;gamma-tubulin binding