NUTM1

Chr 15

NUT midline carcinoma family member 1

Also known as: C15orf55, FAM22H, NUT

NCBI Gene: 256646 ENSG00000184507 UniProt: Q86Y26 OMIM: 608963

Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Jul 2025]

OMIM Research

Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Jul 2025]

OMIM ResearchGenerating clinical summary…

Clinical highlights

Interpreting a novel variant

This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.54

LOEUF

—

Mechanism

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Moderate LoF intolerance

LoF Constraint?

0.54LOEUF

pLI 0.002

Z-score 3.64

OE 0.32 (0.20–0.54)

Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?

0.41Z-score

OE missense 0.95 (0.89–1.02)

594 obs / 622.9 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.32 (0.20–0.54)

0≤0.351.4

Missense OE?0.95 (0.89–1.02)

0≤0.61.4

Synonymous OE?0.90

0≤1.21.6

LoF obs/exp: 11 / 33.9Missense obs/exp: 594 / 622.9Syn Z: 1.22

Background carrier burden — how many people carry a rare variant somewhere in NUTM1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 43

1,469 rare PASS variants

Rare truncating (LoF)

1 in 970

131 rare PASS variants

Rare synonymous (reference)

1 in 120

550 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for NUTM1. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 54	1 in 830
South Asian	~43k	1 in 33	1 in 1,700
Remaining (unassigned)	~30k	1 in 40	1 in 1,200
European (Finnish)	~27k	1 in 90	1 in 1,400
Admixed American	~22k	1 in 33	1 in 2,000
African / African American	~21k	1 in 35	1 in 1,900
East Asian	~20k	1 in 38	1 in 2,200
Ashkenazi Jewish	~13k	1 in 180	≈ 1 in 6,500
Middle Eastern	~2,884	1 in 37	≈ 1 in 2,900

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 7 of 8 coding exons well covered in gnomAD exomes; exon 1 marginal. Genomes: all 8.? see exons ↓