NUTM1

NUT midline carcinoma family member 1

Basic information

Region (hg38): 15:34343314-34357737

Previous symbols: [ "C15orf55" ]

Links

ENSG00000184507 ∙ NCBI:256646 ∙ OMIM:608963 ∙ HGNC:29919 ∙ Uniprot:Q86Y26 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NUTM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUTM1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			50	4	1	55
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1	1	2
Total	0	0	51	5	2

Variants in NUTM1

This is a list of pathogenic ClinVar variants found in the NUTM1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
15-34343396-G-A			Likely benign (Feb 13, 2020)
15-34343662-G-C		not specified	Benign (Mar 29, 2016)
15-34348013-G-A		not specified	Uncertain significance (Jul 28, 2021)
15-34348043-C-G		not specified	Uncertain significance (Nov 18, 2023)
15-34348121-C-T		not specified	Uncertain significance (Jan 04, 2022)
15-34348137-T-A		not specified	Uncertain significance (Feb 14, 2024)
15-34348149-T-C		not specified	Uncertain significance (Jan 08, 2024)
15-34348220-G-A		not specified	Uncertain significance (Nov 08, 2022)
15-34348238-G-T		not specified	Uncertain significance (May 02, 2024)
15-34348299-C-T		not specified	Uncertain significance (Jan 18, 2022)
15-34348358-G-C		not specified	Uncertain significance (Nov 10, 2022)
15-34348395-T-G		not specified	Uncertain significance (Feb 21, 2024)
15-34348512-G-A		not specified	Uncertain significance (Apr 07, 2023)
15-34348544-C-G		not specified	Uncertain significance (Oct 27, 2021)
15-34348559-C-T		not specified	Uncertain significance (Oct 27, 2021)
15-34348580-G-T		not specified	Uncertain significance (Feb 28, 2024)
15-34348587-A-C		not specified	Uncertain significance (Apr 01, 2024)
15-34348595-C-T		not specified	Uncertain significance (Feb 07, 2023)
15-34348600-G-C		not specified	Uncertain significance (May 28, 2024)
15-34348607-C-T		not specified	Uncertain significance (Apr 09, 2022)
15-34348608-G-A		not specified	Uncertain significance (Dec 01, 2022)
15-34348625-C-T		not specified	Uncertain significance (Dec 13, 2022)
15-34350804-C-T		not specified	Uncertain significance (Apr 22, 2022)
15-34350805-G-A		not specified	Uncertain significance (Jun 11, 2024)
15-34353843-C-T		not specified	Uncertain significance (Mar 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUTM1	protein_coding	protein_coding	ENST00000333756	7	14423

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00236	0.998	125678	0	70	125748	0.000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.412	594	623	0.954	0.0000323	7261
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000507	0.000505
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000416	0.000416
European (Non-Finnish)	0.000335	0.000334
Middle Eastern	0.000109	0.000109
South Asian	0.000196	0.000196
Other	0.000165	0.000163

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.103
• hipred: N
• hipred_score: 0.214
• ghis: 0.428

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nutm1

Gene ontology

• Cellular component: nucleus;cytoplasm
• Molecular function: protein binding