RAD54L2

protein-coding

RAD54 like 2

Gene summary

Enables DNA/RNA helicase activity and ubiquitin protein ligase activity. Involved in R-loop processing and transcription elongation by RNA polymerase II. Located in chromatin. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_015106.4

Inheritance

—

ClinVar variants

P:1U:166B:11

Top phenotype

TOP2 deficiency type 1

gnomAD constraint

pLI —, LoF o/e 0.02

Max pathogenic AF

—

Genomic locus

chr3:51,538,719-51,668,667

External References & Databases

Ensembl (ENSG00000164080)

Transcript & Mutation Effects

hg38 • Region Span ~129.9 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 RAD54L2 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 164

not providedTotal: 9

TOP2 deficiency type 1Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015106.4. 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		5 clinvar	6
missense		1 clinvar	162 clinvar	6 clinvar		169
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	1	166	6	5	178

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 33 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015106.4	RefSeq	NP_055921.2	21	MANE Select
ENST00000684192.1	Ensembl	ENSP00000507587.1	21	MANE Select
NM_001322253.2	RefSeq	NP_001309182.1	21	Standard
NM_001322256.2	RefSeq	NP_001309185.1	21	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

DNA binding
helicase activity
protein binding
ATP binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000409535
Coding exons: 21
Length: 127524
Individuals with no LoFs: 125581
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 125584
p: 0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.13	592	849	0.698	0.0000506	9554
Missense (PolyPhen)		119	288.67	0.41224		3201
Synonymous	2.06	283	331	0.856	0.0000193	2975
Loss of Function	7.20	1	62.4	0.0160	0.00000350	715

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000089	0.0000088	rare
South Asian	0.000035	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: DNA helicase that modulates androgen receptor (AR)- dependent transactivation in a promoter-dependent manner. Not able to remodel mononucleosomes in vitro (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.0931

Intolerance Scores

RVIS EVS: -1.39
RVIS percentile EVS: 4.31

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.758

Gene Damage Prediction

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