RAD54B

RAD54 homolog B

Basic information

Region (hg38): 8:94371959-94475115

Links

ENSG00000197275 ∙ NCBI:25788 ∙ OMIM:604289 ∙ HGNC:17228 ∙ Uniprot:Q9Y620 ∙ 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 RAD54B gene.

• Inborn genetic diseases (35 variants)
• not provided (30 variants)
• Non-Hodgkin lymphoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAD54B 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					3	3
missense			31	6	3	40
nonsense						0
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					19	19
Total	0	1	31	6	25

Variants in RAD54B

This is a list of pathogenic ClinVar variants found in the RAD54B region.

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

Position	Type	Phenotype	Significance	ClinVar
8-94372169-AC-A			Likely benign (Dec 31, 2019)
8-94372202-G-C		not specified	Uncertain significance (Jul 25, 2023)
8-94372264-T-C			Likely benign (Jun 29, 2018)
8-94372301-T-C		not specified	Uncertain significance (Jun 24, 2022)
8-94372355-C-T		not specified	Likely benign (Jun 21, 2021)
8-94372360-G-T		not specified	Uncertain significance (Apr 04, 2023)
8-94372364-C-T		not specified	Likely benign (Jun 17, 2022)
8-94372367-T-C		not specified	Uncertain significance (Jun 13, 2023)
8-94378335-C-T		not specified	Uncertain significance (May 23, 2023)
8-94378363-T-C			Likely benign (Jul 04, 2018)
8-94378592-G-A		not specified	Uncertain significance (Nov 18, 2022)
8-94378628-A-G		not specified	Uncertain significance (Aug 26, 2022)
8-94378693-C-T			Benign (Nov 12, 2018)
8-94379827-C-T			Benign (Nov 12, 2018)
8-94380204-T-A		not specified	Uncertain significance (Sep 20, 2023)
8-94380213-G-A		not specified	Uncertain significance (Jul 25, 2023)
8-94380251-A-C		not specified	Uncertain significance (Mar 02, 2023)
8-94380284-A-G		not specified	Uncertain significance (Dec 12, 2023)
8-94380306-T-C		not specified	Likely benign (Jan 26, 2022)
8-94380344-T-C		not specified	Uncertain significance (Feb 14, 2024)
8-94380347-C-T		not specified	Uncertain significance (Jan 08, 2024)
8-94380348-G-A		not specified	Uncertain significance (Dec 12, 2023)
8-94386817-C-T			Benign (Nov 12, 2018)
8-94387003-C-T		not specified	Uncertain significance (Jun 30, 2023)
8-94387014-G-A		not specified	Uncertain significance (Mar 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAD54B	protein_coding	protein_coding	ENST00000336148	14	103150

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.12e-13	0.964	125620	2	123	125745	0.000497

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.925	402	458	0.878	0.0000215	5997
Missense in Polyphen		128	160.15	0.79927		2123
Synonymous	0.682	147	158	0.931	0.00000767	1687
Loss of Function	2.27	26	41.9	0.621	0.00000217	553

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00128	0.00128
Ashkenazi Jewish	0.000102	0.0000992
East Asian	0.000611	0.000598
Finnish	0.00	0.00
European (Non-Finnish)	0.000329	0.000325
Middle Eastern	0.000611	0.000598
South Asian	0.00131	0.00121
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in DNA repair and mitotic recombination. May play an active role in recombination processes in concert with other members of the RAD52 epistasis group. {ECO:0000269|PubMed:11782437, ECO:0000269|PubMed:11884632}.
• Pathway: Homologous recombination - Homo sapiens (human);Homologous recombination (Consensus)

Recessive Scores

• pRec: 0.144

Intolerance Scores

• loftool: 0.198
• rvis_EVS: 0.4
• rvis_percentile_EVS: 76.45

Haploinsufficiency Scores

• pHI: 0.486
• hipred: Y
• hipred_score: 0.610
• ghis: 0.573

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.742

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rad54b
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; hematopoietic system 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)

Gene ontology

• Biological process: double-strand break repair via homologous recombination;mitotic recombination;reciprocal meiotic recombination;DNA duplex unwinding
• Cellular component: nucleus
• Molecular function: DNA binding;DNA helicase activity;RNA helicase activity;protein binding;ATP binding;DNA translocase activity