RAD54B

protein-coding

RAD54 homolog B

Gene summary

The protein encoded by this gene belongs to the DEAD-like helicase superfamily. It shares similarity with Saccharomyces cerevisiae RAD54 and RDH54, both of which are involved in homologous recombination and repair of DNA. This protein binds to double-stranded DNA, and displays ATPase activity in the presence of DNA. This gene is highly expressed in testis and spleen, which suggests active roles in meiotic and mitotic recombination. Homozygous mutations of this gene were observed in primary lymphoma and colon cancer. [provided by RefSeq, Jul 2008]

MANE transcript

NM_012415.3

Inheritance

—

ClinVar variants

P:2U:98B:13

Top phenotype

Carcinoma of colon

gnomAD constraint

pLI —, LoF o/e 0.62

Max pathogenic AF

—

Genomic locus

chr8:94,371,960-94,475,115

External References & Databases

Ensembl (ENSG00000197275)

Transcript & Mutation Effects

hg38 • Region Span ~103.2 kb

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GenCC 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 RAD54B variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 96

not providedTotal: 10

Carcinoma of colonTotal: 1

Non-Hodgkin lymphomaTotal: 1

Colorectal cancerTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_012415.3. 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 clinvar	2 clinvar	3
missense	1 clinvar		95 clinvar	8 clinvar	2 clinvar	106
nonsense						0
start loss						0
frameshift		1 clinvar	1 clinvar			2
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	1	1	98	9	4	113

Highest pathogenic variant AF is 0.000037821155

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 35 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_012415.3	RefSeq	NP_036547.1	14	MANE Select
ENST00000336148.10	Ensembl	ENSP00000336606.5	14	MANE Select
NM_001205262.3	RefSeq	NP_001192191.1	3	Standard
NM_001205263.2	RefSeq	NP_001192192.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Homologous recombination - Homo sapiens (human)
Homologous recombination

Biological Process

double-strand break repair via homologous recombination
mitotic recombination
reciprocal meiotic recombination
DNA duplex unwinding

Molecular Function

DNA binding
DNA helicase activity
RNA helicase activity
protein binding
ATP binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000336148
Coding exons: 14
Length: 103150
Individuals with no LoFs: 125620
Homozygous LoFs: 2
Heterozygous LoFs: 123
Defined: 125745
p: 0.000497

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.925	402	458	0.878	0.0000215	5997
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.00091	0.00090	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00061	0.00060	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00033	0.00033	rare
South Asian	0.0013	0.0012	notable
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.144

Intolerance Scores

LoFtool: 0.198
RVIS EVS: 0.4
RVIS percentile EVS: 76.45

Essentials

Essential (CRISPR): E
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.742

Gene Damage Prediction

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