NUTM1
Chr 15NUT midline carcinoma family member 1
Also known as: C15orf55, FAM22H, NUT
Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Jul 2025]
Clinical Summary— NUTM1
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Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.32) despite low pLI — interpret in context.
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ClinVar Variants
23 Pathogenic / Likely Pathogenic· 159 VUS of 199 total submissions
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Moderate LoF intolerance
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.
0.54LOEUF
pLI 0.002
Z-score 3.64
OE 0.32 (0.20–0.54)
More LoF-intolerant than ~75% of genes
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.
0.41Z-score
OE missense 0.95 (0.89–1.02)
594 obs / 622.9 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.0.32 (0.20–0.54)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.95 (0.89–1.02)
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: 11 / 33.9Missense obs/exp: 594 / 622.9Syn Z: 1.22
ClinVar Variant Classifications
199 submitted variants in ClinVar
Classification Summary
Pathogenic22
Likely Pathogenic1
VUS159
Likely Benign15
Benign2
22
Pathogenic
1
Likely Pathogenic
159
VUS
15
Likely Benign
2
Benign
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 0 | 0 | 22 | 0 | 22 |
Likely Pathogenic | 0 | 0 | 1 | 0 | 1 |
VUS | 1 | 148 | 10 | 0 | 159 |
Likely Benign | 0 | 11 | 4 | 0 | 15 |
Benign | 0 | 2 | 0 | 0 | 2 |
| Total | 1 | 161 | 37 | 0 | 199 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
NUTM1 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
No active trials found for this gene.
Search ClinicalTrials.gov →Clinical Literature
Landmark / reviewRecent case evidence
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
CIC::NUTM1 sarcomas occurred in soft tissues of upper limbs : a rare case report and literature review
Zhao L et al.·Diagn Pathol
2024Review
A characteristic gene expression profile regulated by ACIN1::NUTM1 fusion in a newly identified infant leukaemic cell line and an ACIN1::NUTM1-inducible model
Tamai M et al.·Br J Haematol
2025Functional
NUT Carcinoma: Clinicopathologic Features, Molecular Genetics and Epigenetics
Moreno V et al.·Front Oncol
2022
[The research advances of neoplasm with NUTM1 gene rearrangement].
Yang SM et al.·Zhonghua Bing Li Xue Za Zhi
2022
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
Whole-transcriptome analysis in acute lymphoblastic leukemia: a report from the DFCI ALL Consortium Protocol 16-001.
Tran TH et al.·Blood Adv
2022Clinical trial
Clinical characteristics and outcomes for children, adolescents and young adults with "CIC-fused" or "BCOR-rearranged" soft tissue sarcomas: A multi-institutional European retrospective analysis.
Sparber-Sauer M et al.·Cancer Med
2023
Molecular Characterization of NUT Carcinoma: A Report from the NUT Carcinoma Registry.
Kim JJ et al.·Clin Cancer Res
2025
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Comprehensive Molecular and Functional Analysis of NUTM1-Rearranged Leukemia.
Nishimura K et al.·Blood
2025Functional
Skin-analogue primary poroid neoplasms of the head and neck with YAP1/WWTR1::MAML2/NUTM1 fusions: clinicopathologic and genetic spectrum of a novel tumor family delineated in a series of 10 cases.
Agaimy A et al.·Virchows Arch
2025Cohort
Novel NUTM1 Fusions in Relapsed Acute Myeloid Leukemia: Expanding the Genetic and Clinical Landscape.
Tizro P et al.·Int J Mol Sci
2025Open Access
NSD3::NUTM1 fusion evidenced on RNA sequencing in poorly differentiated thyroid cancer: a report of two cases.
Ciappuccini R et al.·Eur Thyroid J
2025Open AccessCohort
Challenges and Pitfalls to Diagnosing NUTM1-Rearranged Neoplasia of the Pancreas by Cytology and Ancillary Studies.
Lynn TJ.·Diagn Cytopathol
2025
Top 5 resultsSearch Europe PMC ↗
External Resources
Links to major genomics databases and tools