WDR38

protein-coding

WD repeat domain 38, the group of WD repeat domain containing

Gene summary

Predicted to act upstream of or within hematopoietic progenitor cell differentiation. Predicted to be part of transferase complex. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001045476.3

Inheritance

—

ClinVar variants

U:66B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.05

Max pathogenic AF

—

Genomic locus

chr9:124,853,417-124,857,890

External References & Databases

Ensembl (ENSG00000136918)

Transcript & Mutation Effects

hg38 • Region Span ~4.5 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 WDR38 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 70

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001045476.3. 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						0
missense			66 clinvar	5 clinvar		71
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	66	5	0	71

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001045476.3	RefSeq	NP_001038941.1	9	MANE Select
ENST00000373574.2	Ensembl	ENSP00000362677.1	9	MANE Select
NM_001276374.2	RefSeq	NP_001263303.1	9	Standard
NM_001276375.2	RefSeq	NP_001263304.1	9	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000373574
Coding exons: 9
Length: 4406
Individuals with no LoFs: 124665
Homozygous LoFs: 0
Heterozygous LoFs: 150
Defined: 124815
p: 0.000601

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.347	172	185	0.928	0.0000115	2013
Missense (PolyPhen)		58	59.88	0.96861		715
Synonymous	-0.201	79	76.8	1.03	0.00000498	632
Loss of Function	-0.189	16	15.2	1.05	6.54e-7	165

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0031	0.0031	notable
Latino/Admixed American	0.00043	0.00043	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00033	0.00033	rare
Finnish	0.0012	0.0012	notable
European (Non-Finnish)	0.00042	0.00040	rare
South Asian	0.00016	0.00016	rare
Other	0.00083	0.00082	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.106

Intolerance Scores

LoFtool: 0.569
RVIS EVS: 0.73
RVIS percentile EVS: 86.21

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.280

Gene Damage Prediction

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