NUTM2B

Summary

NUTM2B (NUT family member 2B, HGNC:23445) is a protein-coding gene on chromosome 10q22.3, encoding NUT family member 2B (A6NNL0).

At a glance

• Clinical variants (ClinVar): 16 total
• MANE Select transcript: NM_001278495

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23445
Approved symbol	NUTM2B
Name	NUT family member 2B
Location	10q22.3
Locus type	gene with protein product
Status	Approved
Aliases	bA119F19.1
Ensembl gene	ENSG00000188199
Ensembl biotype	protein_coding
Entrez	729262

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000372321, ENST00000429828

RefSeq mRNA: 1 — MANE Select: NM_001278495 NM_001278495

CCDS: CCDS60574

Canonical transcript exons

ENST00000429828 — 7 exons

Exon	Start	End
ENSE00002470831	79703227	79703991
ENSE00002476535	79706042	79706741
ENSE00002509730	79709800	79709939
ENSE00002511836	79708699	79708827
ENSE00002519104	79710382	79710764
ENSE00002526092	79711700	79712758
ENSE00003425445	79711250	79711366

Expression profiles

Bgee: expression breadth ubiquitous, 132 present calls, max score 73.38.

Top tissues by expression

132 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	73.38	gold quality
sural nerve	UBERON:0015488	70.94	gold quality
apex of heart	UBERON:0002098	69.77	gold quality
colonic epithelium	UBERON:0000397	67.99	silver quality
ganglionic eminence	UBERON:0004023	67.32	gold quality
granulocyte	CL:0000094	66.61	gold quality
bone marrow cell	CL:0002092	66.04	silver quality
prefrontal cortex	UBERON:0000451	65.36	gold quality
ventricular zone	UBERON:0003053	64.99	gold quality
bone marrow	UBERON:0002371	64.83	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	64.29	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	63.71	gold quality
frontal cortex	UBERON:0001870	63.45	gold quality
blood	UBERON:0000178	63.07	gold quality
Ammon’s horn	UBERON:0001954	62.43	gold quality
tonsil	UBERON:0002372	62.33	gold quality
temporal lobe	UBERON:0001871	62.25	gold quality
amygdala	UBERON:0001876	62.17	gold quality
cerebral cortex	UBERON:0000956	61.92	gold quality
right lung	UBERON:0002167	61.66	gold quality
right frontal lobe	UBERON:0002810	61.65	gold quality
islet of Langerhans	UBERON:0000006	61.60	gold quality
mucosa of transverse colon	UBERON:0004991	61.51	gold quality
skeletal muscle tissue	UBERON:0001134	61.44	gold quality
adenohypophysis	UBERON:0002196	61.43	gold quality
putamen	UBERON:0001874	61.20	gold quality
anterior cingulate cortex	UBERON:0009835	61.16	gold quality
right atrium auricular region	UBERON:0006631	61.10	gold quality
right testis	UBERON:0004534	61.01	gold quality
pituitary gland	UBERON:0000007	60.97	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.50

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

9 targeting NUTM2B, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-549A-3P	99.54	68.17	825
HSA-MIR-4260	98.78	65.37	848
HSA-MIR-216B-3P	98.55	67.19	1223
HSA-MIR-637	97.91	64.05	1517
HSA-MIR-1225-3P	97.29	64.60	876

Literature-anchored findings (GeneRIF, showing 3)

• Tumors with YWHAE-FAM22 rearrangements constitute a distinct group of endometrial stromal sarcoma (ESS), which is associated with high-grade morphology and aggressive clinical behavior compared to JAZF1 ESS. (PMID:22456610)
• Studies show that patients with clear cell sarcoma of the kidney (CCSK) and the fusion YWHAE-NUTM2B/E were relatively young, had low tumor volumes, and did not present with stage I disease which fail to identify an explicit clinical phenotype. (PMID:26542179)
• we report recurrent BCOR exon 16 internal tandem duplications and YWHAE-NUTM2B fusions in half of infantile soft tissue undifferentiated round cell sarcoma and most primitive myxoid mesenchymal tumor of infancy cases, but not in other pediatric sarcomas. (PMID:26945340)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Nutm2	ENSMUSG00000071909
rattus_norvegicus	Nutm2	ENSRNOG00000027311

Paralogs (6): NUTM2F (ENSG00000130950), NUTM1 (ENSG00000184507), NUTM2A (ENSG00000184923), NUTM2G (ENSG00000188152), NUTM2D (ENSG00000214562), NUTM2E (ENSG00000228570)

Protein

Protein identifiers

NUT family member 2B — A6NNL0 (reviewed: A6NNL0)

All UniProt accessions (2): A0A0A0MRQ8, A6NNL0

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the NUT family.

Isoforms (2)

UniProt ID	Names	Canonical?
A6NNL0-1	1	yes
A6NNL0-2	2

RefSeq proteins (1): NP_001265424* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR024309	NUT_N	Domain
IPR024310	NUT	Family

Pfam: PF12881

UniProt features (14 total): region of interest 6, compositionally biased region 4, splice variant 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NNL0-F1	46.50	0.06

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 6 (showing top): MIR637, MIR4260, GSE17974_IL4_AND_ANTI_IL12_VS_UNTREATED_1H_ACT_CD4_TCELL_UP, PULVER_FOREY_CELLCYCLE_PEAKING_M, GSE29617_CTRL_VS_DAY3_TIV_FLU_VACCINE_PBMC_2008_DN, chr10q22

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

506 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NUTM2B	YWHAE	P29360	772
NUTM2B	CCNB3	Q8WWL7	647
NUTM2B	ZC3H7B	Q9UGR2	603
NUTM2B	JAZF1	Q86VZ6	542
NUTM2B	BCOR	Q6W2J9	473
NUTM2B	H3BVE0	H3BVE0	446
NUTM2B	MEAF6	Q9HAF1	422
NUTM2B	PHF1	O43189	403
NUTM2B	DUX4L2	P0CJ85	399
NUTM2B	IRX2	Q9BZI1	367
NUTM2B	RSPH10B2	B2RC85	360
NUTM2B	EZHIP	Q86X51	333
NUTM2B	SATB2	Q9UPW6	326
NUTM2B	LIMS3	P0CW19	321
NUTM2B	MBTD1	Q05BQ5	319

IntAct

0 interactions, top by confidence:

BioGRID (4): NUTM2B (Affinity Capture-MS), NUTM2B (Affinity Capture-MS), NUTM2B (Affinity Capture-MS), NUTM2B (Two-hybrid)

ESM2 similar proteins: A0A096LP49, A0A8V8TNH8, A0A8V8TPE2, A1L443, A2IDD5, A5D7L8, A6NDY2, A6NIJ5, A6NNJ1, A6NNL0, A7E346, A8K0R7, A8MXJ8, A8MXZ1, B1AL46, B1ASB6, C9JSJ3, E9PGG2, O08574, P0C7V4, P0C7W8, P0C7X0, P0CG20, P0DV73, P0DV75, P0DV76, Q0VG99, Q0ZCJ7, Q149B8, Q2M3G4, Q3TQ03, Q3V0C3, Q4KLY2, Q5JXC2, Q5RCJ6, Q5SV97, Q5SW24, Q5VT03, Q5VZR2, Q6ZMY3

Diamond homologs: A1L443, A6NNL0, B1AL46, Q3V0C3, Q5VT03, Q5VZR2, Q86Y26, Q8BHP2, Q8IVF1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

16 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	2
Likely benign	10
Benign	3

Top pathogenic / likely-pathogenic (0)

SpliceAI

1258 predictions. Top by Δscore:

Variant	Effect	Δscore
10:79708697:A:AG	acceptor_gain	1.0000
10:79708697:A:G	acceptor_loss	1.0000
10:79708698:G:GT	acceptor_gain	1.0000
10:79708698:GC:G	acceptor_gain	1.0000
10:79708698:GCC:G	acceptor_gain	1.0000
10:79708698:GCCC:G	acceptor_gain	1.0000
10:79708698:GCCCA:G	acceptor_gain	1.0000
10:79708823:GAAAA:G	donor_gain	1.0000
10:79708824:AAAA:A	donor_gain	1.0000
10:79708825:AAA:A	donor_gain	1.0000
10:79708826:AA:A	donor_gain	1.0000
10:79708827:AGTG:A	donor_loss	1.0000
10:79708828:G:GG	donor_gain	1.0000
10:79710381:GT:G	acceptor_gain	1.0000
10:79711241:T:TA	acceptor_gain	1.0000
10:79711245:TCCA:T	acceptor_loss	1.0000
10:79711246:CCA:C	acceptor_loss	1.0000
10:79711247:CA:C	acceptor_loss	1.0000
10:79711248:A:AC	acceptor_loss	1.0000
10:79711248:A:AG	acceptor_gain	1.0000
10:79711248:AG:A	acceptor_gain	1.0000
10:79711248:AGGT:A	acceptor_gain	1.0000
10:79711248:AGGTG:A	acceptor_gain	1.0000
10:79711249:G:GT	acceptor_gain	1.0000
10:79711249:GG:G	acceptor_gain	1.0000
10:79711249:GGT:G	acceptor_gain	1.0000
10:79711249:GGTG:G	acceptor_gain	1.0000
10:79711249:GGTGG:G	acceptor_gain	1.0000
10:79711343:G:GT	donor_gain	1.0000
10:79711346:G:GT	donor_gain	1.0000

AlphaMissense

5613 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:79706734:T:C	F359L	0.992
10:79706736:C:A	F359L	0.992
10:79706736:C:G	F359L	0.992
10:79708777:G:C	W387C	0.992
10:79708777:G:T	W387C	0.992
10:79709801:T:C	F405L	0.990
10:79709803:C:A	F405L	0.990
10:79709803:C:G	F405L	0.990
10:79708775:T:A	W387R	0.989
10:79708775:T:C	W387R	0.989
10:79708808:T:C	F398L	0.985
10:79708810:C:A	F398L	0.985
10:79708810:C:G	F398L	0.985
10:79706665:T:A	W336R	0.983
10:79706665:T:C	W336R	0.983
10:79706667:G:C	W336C	0.980
10:79706667:G:T	W336C	0.980
10:79709802:T:C	F405S	0.980
10:79709810:T:C	F408L	0.978
10:79709812:T:A	F408L	0.978
10:79709812:T:G	F408L	0.978
10:79706656:T:C	F333L	0.976
10:79706658:C:A	F333L	0.976
10:79706658:C:G	F333L	0.976
10:79706687:C:A	A343D	0.976
10:79708776:G:C	W387S	0.974
10:79706679:G:C	K340N	0.973
10:79706679:G:T	K340N	0.973
10:79708763:G:C	A383P	0.971
10:79706735:T:C	F359S	0.969

dbSNP variants (sampled 300 via entrez): RS1000137300 (10:79694283 G>A), RS1000190765 (10:79697074 C>T), RS1000237740 (10:79691061 C>A,T), RS1000626314 (10:79697520 A>G), RS1000713405 (10:79709491 G>T), RS1001899321 (10:79695775 G>A), RS1002035125 (10:79690246 T>C), RS1002415764 (10:79704928 T>C), RS1003068863 (10:79699719 A>G), RS1003542350 (10:79694408 A>G), RS1003981641 (10:79694663 G>C), RS1004806321 (10:79694878 C>T), RS1005405185 (10:79699019 G>A), RS1005450672 (10:79691816 C>T), RS1005483153 (10:79692090 C>T)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:618637

GenCC curated gene-disease

Mondo (1): oculopharyngeal myopathy with leukoencephalopathy 1 (MONDO:0032843)

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

6 total (human), top 6 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
2,6-dichloro-(1,4)benzoquinone	increases expression	1
Thiram	increases expression	1
Tobacco Smoke Pollution	increases expression	1
Acrylamide	increases expression	1
p-Chloromercuribenzoic Acid	increases expression	1
S-Nitrosoglutathione	increases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.