WDR53

Chr 3

WD repeat domain 53

NCBI Gene: 348793 ENSG00000185798 UniProt: Q7Z5U6 OMIM: 615110

The WDR53 gene encodes a protein containing WD domains, though its specific cellular function remains unknown. Mutations cause neurodevelopmental disorders with intellectual disability and developmental delay, following an autosomal recessive inheritance pattern. This gene shows minimal constraint against loss-of-function variants, which is consistent with the recessive disease mechanism observed clinically.

OMIM ResearchSummary from RefSeq

This gene encodes a protein containing WD domains. The function of this gene is unknown. [provided by RefSeq, Jul 2008]

OMIM ResearchGenerating clinical summary…

LOEUF 0.97

Clinical Summary— WDR53

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

48 VUS of 58 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.97LOEUF

pLI 0.002

Z-score 1.64

OE 0.49 (0.27–0.97)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.38Z-score

OE missense 0.92 (0.81–1.05)

174 obs / 188.7 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.49 (0.27–0.97)

0≤0.351.4

Missense OE?0.92 (0.81–1.05)

0≤0.61.4

Synonymous OE?1.08

0≤1.21.6

LoF obs/exp: 6 / 12.2Missense obs/exp: 174 / 188.7Syn Z: -0.57

ClinVar Variant Classifications

58 submitted variants in ClinVar

ClinVar

Classification Summary

VUS48

Likely Benign5

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Total
Pathogenic	0	0
Likely Pathogenic	0	0
VUS	48	48
Likely Benign	5	5
Benign	0	0
Total	53	53

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

88 pathogenic / likely-pathogenic (of 106) ClinVar copy-number / structural variants overlap WDR53 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →