WDR90

protein-coding

WD repeat domain 90, the group of WD repeat domain containing

Gene summary

Enables microtubule binding activity. Involved in centriole elongation and cilium assembly. Located in centriolar satellite; centriole; and ciliary basal body. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C16orf17
C16orf15
C16orf16
C16orf19
C16orf18

MANE transcript

NM_145294.5

Inheritance

—

ClinVar variants

U:410B:60

Top phenotype

Autism

gnomAD constraint

pLI —, LoF o/e 1.09

Max pathogenic AF

—

Genomic locus

chr16:649,311-667,833

External References & Databases

Ensembl (ENSG00000161996)

Transcript & Mutation Effects

hg38 • Region Span ~18.5 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 WDR90 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 422

not providedTotal: 18

AutismTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_145294.5. 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			9 clinvar	8 clinvar	1 clinvar	18
missense			382 clinvar	50 clinvar	1 clinvar	433
nonsense			3 clinvar			3
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			16 clinvar			16
Total	0	0	410	58	2	470

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 80 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_145294.5	RefSeq	NP_660337.3	41	MANE Select
ENST00000293879.9	Ensembl	ENSP00000293879.4	41	MANE Select
NM_001438707.1	RefSeq	NP_001425636.1	42	Standard
NM_001438708.1	RefSeq	NP_001425637.1	42	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cilium assembly

Molecular Function

protein binding

Cellular Component

centriole

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000293879
Coding exons: 41
Length: 18523
Individuals with no LoFs: 124268
Homozygous LoFs: 4
Heterozygous LoFs: 658
Defined: 124930
p: 0.00265

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.926	1208	1.12e+3	1.08	0.0000755	11093
Missense (PolyPhen)		415	379.27	1.0942		4130
Synonymous	-4.84	649	510	1.27	0.0000389	3703
Loss of Function	-0.785	93	85.2	1.09	0.00000435	874

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0029	0.0026	notable
Latino/Admixed American	0.0072	0.0071	notable
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.0021	0.0020	notable
Finnish	0.00055	0.00051	rare
European (Non-Finnish)	0.0025	0.0023	notable
South Asian	0.0019	0.0018	notable
Other	0.0017	0.0016	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Required for efficient primary cilium formation. {ECO:0000269|PubMed:28781053}.;

Intolerance Scores

LoFtool: 0.934
RVIS EVS: 0.97
RVIS percentile EVS: 90.28

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.476

Gene Damage Prediction

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