UTP6
Chr 17UTP6 small subunit processome component
Also known as: C17orf40, HCA66
Predicted to enable snoRNA binding activity. Involved in ribosomal small subunit biogenesis. Located in chromosome and nucleolus. Part of small-subunit processome. [provided by Alliance of Genome Resources, Jul 2025]
Clinical Summary— UTP6
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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
44 Pathogenic / Likely Pathogenic· 82 VUS of 134 total submissions
Some data sources returned errors (1)
ensembl: TimeoutError: The operation was aborted due to timeout
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.67LOEUF
pLI 0.000
Z-score 3.30
OE 0.46 (0.32–0.67)
Typical tolerance to LoF variation
Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
0.44Z-score
OE missense 0.93 (0.84–1.02)
292 obs / 314.1 exp
Mild missense constraint
Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.46 (0.32–0.67)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.93 (0.84–1.02)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.90
0≤1.21.6
LoF obs/exp: 20 / 43.5Missense obs/exp: 292 / 314.1Syn Z: 0.86
ClinVar Variant Classifications
134 submitted variants in ClinVar
Classification Summary
Pathogenic42
Likely Pathogenic2
VUS82
Likely Benign4
Benign4
42
Pathogenic
2
Likely Pathogenic
82
VUS
4
Likely Benign
4
Benign
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 0 | 0 | 42 | 0 | 42 |
Likely Pathogenic | 0 | 0 | 2 | 0 | 2 |
VUS | 0 | 76 | 6 | 0 | 82 |
Likely Benign | 0 | 3 | 1 | 0 | 4 |
Benign | 0 | 2 | 0 | 2 | 4 |
| Total | 0 | 81 | 51 | 2 | 134 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
UTP6 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
OMIM — Genotype-Phenotype Relationships
1 OMIM entry
UTP6 SMALL SUBUNIT PROCESSOME COMPONENT; UTP6
MIM #620948 · *
External Resources
Links to major genomics databases and tools
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
SISH/CISH or qPCR as alternative techniques to FISH for determination of HER2 amplification status on breast tumors core needle biopsies: a multicenter experience based on 840 cases.
Jacquemier J et al.·BMC Cancer
2013Cohort
NF1 microdeletion syndrome: case report of two new patients.
Serra G et al.·Ital J Pediatr
2019Case report
Identification of epigenetic interactions between miRNA and DNA methylation associated with gene expression as potential prognostic markers in bladder cancer.
Shivakumar M et al.·BMC Med Genomics
2017
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Hypermethylation and Downregulation of UTP6 Are Associated With Stemness Properties, Chemoradiotherapy Resistance, and Prognosis in Rectal Cancer: A Co-expression Network Analysis.
Zhang Y et al.·Front Cell Dev Biol
2021Open Access
A structural model for the HAT domain of Utp6 incorporating bioinformatics and genetics.
Champion EA et al.·Protein Eng Des Sel
2009Functional
Top 5 resultsSearch Europe PMC ↗
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
Identification of novel immune infiltration-related biomarkers of sepsis based on bioinformatics analysis.
Li H et al.·Cell Mol Biol (Noisy-le-grand)
2023
Differentially localized protein identification for breast cancer based on deep learning in immunohistochemical images.
Zhang Z et al.·Commun Biol
2024
4D-DIA quantitative proteomics revealed the core mechanism of diabetic retinopathy after berberine treatment.
Na L et al.·Eur J Pharmacol
2023Functional
Transcriptomic Response Pathways of Yeast to Crucial Polyphenolic Acids in Rosmarinus Acid Biosynthesis.
Xu T et al.·Curr Microbiol
2025
Proteogenomic Analysis Identifies Clinically Relevant Subgroups of Collecting Duct Carcinoma.
Qu Y et al.·Research (Wash D C)
2025
Comparative analysis of muscle structure and weighted gene co-expression network analysis reveals growth mechanisms in fast-growing and slow-growing silver pomfret (Pampus argenteus).
Li C et al.·J Fish Biol
2025Functional
A Homologous Recombination System to Generate Epitope-Tagged Target Genes in Chaetomium thermophilum: A Genetic Approach to Investigate Native Thermostable Proteins
Kellner N et al.·Int J Mol Sci
2022
Evidence that conserved essential genes are enriched for pro-longevity factors
Oz N et al.·Geroscience
2022
Top 9 full-text resultsSearch PubTator3 ↗
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
No active trials found for this gene.
Search ClinicalTrials.gov →External Resources
Links to major genomics databases and tools