WDR89

protein-coding

WD repeat domain 89, the group of WD repeat domain containing

Gene summary

Predicted to act upstream of or within corpus callosum development and ventricular system development. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C14orf150

MANE transcript

NM_080666.4

Inheritance

—

ClinVar variants

U:50B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.66

Max pathogenic AF

—

Genomic locus

chr14:63,597,039-63,641,871

External References & Databases

Ensembl (ENSG00000140006)

Transcript & Mutation Effects

hg38 • Region Span ~44.8 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 WDR89 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 55

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_080666.4. 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						0
missense			50 clinvar	5 clinvar		55
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	50	5	0	55

Loading ClinVar variants...

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_080666.4	RefSeq	NP_542397.1	1	MANE Select
ENST00000620954.2	Ensembl	ENSP00000480112.1	1	MANE Select
NM_001008726.3	RefSeq	NP_001008726.1	1	Standard
NM_001258272.2	RefSeq	NP_001245201.1	1	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000394942
Coding exons: 1
Length: 44823
Individuals with no LoFs: 125645
Homozygous LoFs: 0
Heterozygous LoFs: 101
Defined: 125746
p: 0.000402

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.884	167	202	0.825	0.00000949	2556
Missense (PolyPhen)		22	37.507	0.58656		468
Synonymous	0.141	69	70.5	0.979	0.00000303	742
Loss of Function	1.10	8	12.1	0.659	6.74e-7	163

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.00026	0.00026	rare
Ashkenazi Jewish	0.0016	0.0016	notable
East Asian	0.00011	0.00011	rare
Finnish	0.00028	0.00028	rare
European (Non-Finnish)	0.00037	0.00035	rare
South Asian	0.00065	0.00065	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0962

Intolerance Scores

LoFtool: 0.871
RVIS EVS: -0.54
RVIS percentile EVS: 20.26

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): H
Indispensability pred.: E
Indispensability score: 0.859

Gene Damage Prediction

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