GeneBe

RAD51D

RAD51 paralog D

Basic information

Region (hg38): 17:35092221-35121522

Previous symbols: [ "RAD51L3" ]

Links

ENSG00000185379 ∙ NCBI:5892 ∙ OMIM:602954 ∙ HGNC:9823 ∙ Uniprot:O75771 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • 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
  • hereditary breast carcinoma (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Breast-ovarian cancer, familial, susceptibility to, 4ADOncologicSurveillance (similar to that described for individuals with variants in BRCA1 or BRCA2) related to breast or ovarian cancer may allow early diagnosis and treatment of neoplasms (eg, ovarian tumors), which may reduce morbidity and mortality; Specific, targeted therapies may be availableOncologic21822267; 23300655; 23372765

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RAD51D gene.

  • Breast-ovarian_cancer,_familial,_susceptibility_to,_4 (1554 variants)
  • Hereditary_cancer-predisposing_syndrome (1185 variants)
  • not_provided (347 variants)
  • not_specified (192 variants)
  • Hereditary_breast_ovarian_cancer_syndrome (92 variants)
  • RAD51D-related_disorder (47 variants)
  • Familial_ovarian_cancer (34 variants)
  • Breast_and/or_ovarian_cancer (33 variants)
  • Malignant_tumor_of_breast (32 variants)
  • Gastric_cancer (13 variants)
  • Hereditary_cancer (8 variants)
  • Ovarian_neoplasm (8 variants)
  • RAD51D-related_cancer_predisposition (7 variants)
  • Breast-ovarian_cancer,_familial,_susceptibility_to,_1 (3 variants)
  • Deleterious_RAD51D_Gene_Mutation (3 variants)
  • Ovarian_carcinoma (3 variants)
  • Inherited_ovarian_cancer_(without_breast_cancer) (3 variants)
  • Inherited_breast_cancer_and_ovarian_cancer (2 variants)
  • Hereditary_site-specific_ovarian_cancer_syndrome (2 variants)
  • Familial_cancer_of_breast (2 variants)
  • Cancer_or_benign_tumor (1 variants)
  • Breast-ovarian_cancer,_familial,_susceptibility_to,_3 (1 variants)
  • Diffuse_midline_glioma,_H3_K27-altered (1 variants)
  • Breast_carcinoma (1 variants)
  • Lynch_syndrome_1 (1 variants)
  • Breast_cancer,_susceptibility_to (1 variants)
  • Carcinoma_of_colon (1 variants)
  • See_cases (1 variants)
  • Colorectal_cancer (1 variants)
  • Childhood_neoplasm (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. These statistics are base on transcript: NM_000002878.4. 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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
3
clinvar
12
clinvar
323
clinvar
43
clinvar
 382
missense
4
clinvar
8
clinvar
771
clinvar
55
clinvar
3
clinvar
 841
nonsense
35
clinvar
17
clinvar
8
clinvar
 60
start loss
9
1
 10
frameshift
81
clinvar
61
clinvar
13
clinvar
 155
splice donor/acceptor (+/-2bp)
3
clinvar
60
clinvar
9
clinvar
 72
Total 124 158 814 378 46

Highest pathogenic variant AF is 0.000031598593

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RAD51Dprotein_codingprotein_codingENST00000590016 1021731
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
1.06e-90.3141256950531257480.000211
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.1121981941.020.00001152194
Missense in Polyphen6057.7891.0383708
Synonymous-0.04298180.51.010.00000492755
Loss of Function0.8201620.00.8020.00000123199

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002710.000271
Ashkenazi Jewish0.0007010.000695
East Asian0.0008700.000870
Finnish0.000.00
European (Non-Finnish)0.0001680.000149
Middle Eastern0.0008700.000870
South Asian0.0001960.000196
Other0.0001630.000163

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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