UTP11

Chr 1

UTP11 small subunit processome component

Also known as: CGI-94, CGI94, UTP11L

NCBI Gene: 51118 ENSG00000183520 UniProt: Q9Y3A2 OMIM: 609440

UTP11 encodes a protein that is part of the small subunit processome and is essential for ribosomal small subunit biogenesis, specifically involved in nucleolar processing of pre-18S ribosomal RNA. Mutations cause microcephaly with early-onset seizures and severe developmental delay, inherited in an autosomal recessive pattern. The gene shows minimal constraint against loss-of-function variants, which is consistent with the recessive inheritance pattern observed in affected patients.

OMIM ResearchSummary from RefSeq, UniProt

Enables RNA binding activity. Involved in nervous system development; positive regulation of apoptotic process; and ribosomal small subunit biogenesis. Located in cytosol; extracellular space; and nuclear lumen. Part of small-subunit processome. [provided by Alliance of Genome Resources, Jul 2025]

OMIM ResearchGenerating clinical summary…

DNmechanismLOEUF 1.18

Clinical Summary— UTP11

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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

4 VUS of 18 total submissions

Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.18LOEUF

pLI 0.000

Z-score 1.01

OE 0.74 (0.48–1.18)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.42Z-score

OE missense 0.90 (0.78–1.04)

129 obs / 143.2 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.74 (0.48–1.18)

0≤0.351.4

Missense OE?0.90 (0.78–1.04)

0≤0.61.4

Synonymous OE?1.07

0≤1.21.6

LoF obs/exp: 13 / 17.6Missense obs/exp: 129 / 143.2Syn Z: -0.40

This gene — mechanism propensity

0.7230th %ile

GOF

0.3986th %ile

LOF

0.3162th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

18 submitted variants in ClinVar

ClinVar

Classification Summary

VUS4

VUS

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Total
Pathogenic	0	0
Likely Pathogenic	0	0
VUS	4	4
Likely Benign	0	0
Benign	0	0
Total	4	4

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

View in ClinVar →

5 pathogenic / likely-pathogenic (of 10) ClinVar copy-number / structural variants overlap UTP11 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →