WDFY4

protein-coding

WDFY family member 4, the group of BEACH domain containing |WD repeat domain containing|Armadillo like helical domain containing

Gene summary

Predicted to be involved in antigen processing and presentation. Predicted to act upstream of or within with a positive effect on CD8-positive, alpha-beta T cell activation. Predicted to act upstream of or within cellular response to virus. Predicted to be located in early endosome and endoplasmic reticulum. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C10orf64

MANE transcript

NM_001394531.1

Inheritance

ClinVar variants

U:485B:49

Top phenotype

WDFY4-related disorder

gnomAD constraint

pLI —, LoF o/e 0.23

Max pathogenic AF

—

Genomic locus

chr10:48,684,873-48,982,956

External References & Databases

Ensembl (ENSG00000128815)

Transcript & Mutation Effects

hg38 • Region Span ~298.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

complex neurodevelopmental disorderLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0100038

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to WDFY4 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 550

WDFY4-related disorderTotal: 24

not providedTotal: 15

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001394531.1. 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	6 clinvar	3 clinvar	11
missense			479 clinvar	35 clinvar	5 clinvar	519
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	485	41	8	534

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001394531.1	RefSeq	NP_001381460.1	61	MANE Select
ENST00000325239.12	Ensembl	ENSP00000320563.5	61	MANE Select
NM_001370153.1	RefSeq	NP_001357082.1	28	Standard
NM_001370154.1	RefSeq	NP_001357083.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000325239
Coding exons: 61
Length: 298081
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.12	1319	1.68e+3	0.785	0.0000931	20668
Missense (PolyPhen)		321	503.31	0.63778		6515
Synonymous	1.90	643	707	0.909	0.0000422	6405
Loss of Function	8.63	33	145	0.227	0.00000679	1766

Population LoF Frequency

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

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0993

Intolerance Scores

RVIS EVS: 4.26
RVIS percentile EVS: 99.72

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.185

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High