NUTM1

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			151 clinvar	11 clinvar	1 clinvar	163
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	152	11	1	164

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001284292.2	RefSeq	NP_001271221.2	8	MANE Select
ENST00000537011.6	Ensembl	ENSP00000444896.1	8	MANE Select
NM_001284293.2	RefSeq	NP_001271222.2	7	Standard
NM_175741.3	RefSeq	NP_786883.2	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

Cellular Component

nucleus
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000333756
Coding exons: 7
Length: 14423
Individuals with no LoFs: 125678
Homozygous LoFs: 0
Heterozygous LoFs: 70
Defined: 125748
p: 0.000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.412	594	623	0.954	0.0000323	7261
Missense (PolyPhen)		93	111.48	0.8342		1428
Synonymous	1.22	216	240	0.900	0.0000123	2458
Loss of Function	3.64	11	33.9	0.325	0.00000153	427

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.00032	0.00032	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.00042	0.00042	rare
European (Non-Finnish)	0.00034	0.00033	rare
South Asian	0.00020	0.00020	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Disease: DISEASE: Note=A chromosomal aberration involving NUT is found in a rare, aggressive, and lethal carcinoma arising in midline organs of young people. Translocation t(15;19)(q14;p13) with BRD4 which produces a BRD4-NUT fusion protein. {ECO:0000269|PubMed:12543779}.; DISEASE: Note=A chromosomal aberration involving NUT is found in a rare, aggressive, and lethal carcinoma arising in midline organs of young people. Translocation t(15;9)(q14;q34) with BRD3 which produces a BRD3-NUT fusion protein. {ECO:0000269|PubMed:12543779}.;

Recessive Scores

pRec: 0.0889

Intolerance Scores

RVIS EVS: 1.43
RVIS percentile EVS: 95.02

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium