RAD51AP1

RAD51 associated protein 1

Basic information

Region (hg38): 12:4538798-4560047

Links

ENSG00000111247 ∙ NCBI:10635 ∙ OMIM:603070 ∙ HGNC:16956 ∙ Uniprot:Q96B01 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RAD51AP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAD51AP1 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			17	3	3	23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	17	3	4

Variants in RAD51AP1

This is a list of pathogenic ClinVar variants found in the RAD51AP1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-4541894-C-G			Benign (Jun 05, 2018)
12-4541932-T-C			Benign (Jun 05, 2018)
12-4543873-A-C		not specified	Uncertain significance (May 06, 2024)
12-4543897-A-C			Benign (May 16, 2018)
12-4545773-T-C			Benign (May 16, 2018)
12-4546323-A-T		not specified	Uncertain significance (Mar 08, 2024)
12-4546374-A-G		not specified	Uncertain significance (Dec 28, 2023)
12-4548135-G-C		not specified	Uncertain significance (Dec 14, 2023)
12-4548710-G-A		not specified	Uncertain significance (Aug 16, 2022)
12-4548720-G-A		not specified	Uncertain significance (Oct 04, 2022)
12-4548769-G-C		not specified	Uncertain significance (May 25, 2022)
12-4548783-T-C		not specified	Uncertain significance (Mar 20, 2023)
12-4548830-G-A		not specified	Uncertain significance (Aug 20, 2023)
12-4548833-C-T		not specified	Uncertain significance (Jun 22, 2023)
12-4553033-G-A		not specified	Uncertain significance (Mar 21, 2024)
12-4553043-C-T		not specified	Uncertain significance (Jun 16, 2024)
12-4553045-A-G		not specified	Likely benign (Mar 04, 2024)
12-4553054-A-T			Likely benign (Jun 18, 2018)
12-4553055-G-C		not specified	Uncertain significance (Oct 03, 2022)
12-4553133-A-G		not specified	Uncertain significance (Mar 11, 2022)
12-4556353-T-C		not specified	Uncertain significance (Jan 23, 2023)
12-4556493-G-A		not specified	Uncertain significance (Sep 17, 2021)
12-4558863-C-T		not specified	Uncertain significance (Aug 02, 2021)
12-4558865-G-A			Benign (Jun 18, 2018)
12-4558902-T-C		not specified	Uncertain significance (Aug 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAD51AP1	protein_coding	protein_coding	ENST00000228843	10	21265

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0111	0.981	125735	1	11	125747	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.469	160	178	0.901	0.00000845	2321
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000211	0.000211
Ashkenazi Jewish	0.00	0.00
East Asian	0.000118	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000445	0.0000439
Middle Eastern	0.000118	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• 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}.
• Pathway: 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;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)

Recessive Scores

• pRec: 0.0852

Intolerance Scores

• loftool: 0.930
• rvis_EVS: 0.91
• rvis_percentile_EVS: 89.47

Haploinsufficiency Scores

• pHI: 0.343
• hipred: Y
• hipred_score: 0.592
• ghis: 0.515

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.601

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Rad51ap1

Gene ontology

• 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
• Cellular component: nuclear chromatin;nucleus;nucleoplasm;protein-containing complex
• Molecular function: double-stranded DNA binding;single-stranded DNA binding;RNA binding;protein binding