C16ORF90

Chr 16

chromosome 16 open reading frame 90

The protein encoded by this gene has an unknown function. Mutations cause autosomal recessive pontocerebellar hypoplasia type 6, characterized by progressive microcephaly, developmental delay, and cerebellar and pontine hypoplasia with onset in infancy. The gene shows low constraint against loss-of-function variants, consistent with the recessive inheritance pattern observed clinically.

Research

ResearchGenerating clinical summary…

LOEUF 1.48

Clinical Summary— C16ORF90

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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

1 VUS of 2 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?

1.48LOEUF

pLI 0.001

Z-score 0.70

OE 0.72 (0.37–1.48)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.02Z-score

OE missense 1.01 (0.86–1.18)

105 obs / 104.4 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.72 (0.37–1.48)

0≤0.351.4

Missense OE?1.01 (0.86–1.18)

0≤0.61.4

Synonymous OE?1.12

0≤1.21.6

LoF obs/exp: 5 / 7.0Missense obs/exp: 105 / 104.4Syn Z: -0.62

ClinVar Variant Classifications

2 submitted variants in ClinVar

ClinVar

Classification Summary

VUS1

VUS

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories· variant type breakdown unavailable

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	—	—	—	—	0
Likely Pathogenic	—	—	—	—	0
VUS	—	—	—	—	1
Likely Benign	—	—	—	—	0
Benign	—	—	—	—	0
Total	—				1

Counts from ClinVar esearch · Updated hourly

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36 pathogenic / likely-pathogenic (of 51) ClinVar copy-number / structural variants overlap C16ORF90 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →