WDR76

protein-coding

WD repeat domain 76, the group of WD repeat domain containing

Gene summary

Enables enzyme binding activity. Involved in DNA damage response. Located in heterochromatin; nucleus; and site of DNA damage. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_024908.4

Inheritance

—

ClinVar variants

U:93B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.58

Max pathogenic AF

—

Genomic locus

chr15:43,826,980-43,868,412

External References & Databases

Ensembl (ENSG00000092470)

Transcript & Mutation Effects

hg38 • Region Span ~41.4 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 WDR76 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 91

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024908.4. 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			2 clinvar			2
missense			88 clinvar	4 clinvar		92
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	93	4	0	97

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024908.4	RefSeq	NP_079184.2	13	MANE Select
ENST00000263795.11	Ensembl	ENSP00000263795.6	13	MANE Select
NM_001167941.2	RefSeq	NP_001161413.1	12	Standard
ENST00000381246.6	Ensembl	ENSP00000370645.2	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cellular response to DNA damage stimulus
regulation of DNA damage checkpoint

Molecular Function

DNA binding
protein binding
enzyme binding

Cellular Component

heterochromatin
nucleus
site of DNA damage

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000263795
Coding exons: 13
Length: 41457
Individuals with no LoFs: 125668
Homozygous LoFs: 0
Heterozygous LoFs: 79
Defined: 125747
p: 0.000314

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.462	320	344	0.930	0.0000177	4098
Missense (PolyPhen)		47	67.942	0.69177		710
Synonymous	-0.208	131	128	1.02	0.00000718	1201
Loss of Function	2.22	19	32.7	0.581	0.00000183	393

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.00052	0.00052	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00033	0.00033	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00033	0.00033	rare
South Asian	0.00026	0.00026	rare
Other	0.00066	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Specifically binds 5-hydroxymethylcytosine (5hmC), suggesting that it acts as a specific reader of 5hmC. {ECO:0000250}.;

Recessive Scores

pRec: 0.0932

Intolerance Scores

LoFtool: 0.244
RVIS EVS: 0.04
RVIS percentile EVS: 57.31

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.932

Gene Damage Prediction

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