NUTM2D

Summary

NUTM2D (NUT family member 2D, HGNC:23447) is a protein-coding gene on chromosome 10q23.2, encoding NUT family member 2D (Q5VT03).

At a glance

• Clinical variants (ClinVar): 6 total
• Cancer driver (intOGen): activating (oncogene-like) across 1 cancer types
• MANE Select transcript: NM_001382304

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23447
Approved symbol	NUTM2D
Name	NUT family member 2D
Location	10q23.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000214562
Ensembl biotype	protein_coding
Entrez	728130

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000381697, ENST00000412718, ENST00000465545

RefSeq mRNA: 2 — MANE Select: NM_001382304 NM_001009610, NM_001382304

CCDS: CCDS91292

Canonical transcript exons

ENST00000381697 — 7 exons

Exon	Start	End
ENSE00001489535	87366139	87367195
ENSE00002430792	87364239	87364378
ENSE00002431928	87365689	87365805
ENSE00002463267	87360481	87361180
ENSE00002502210	87364821	87365203
ENSE00002515316	87363138	87363266
ENSE00002709224	87357744	87358431

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 82.40.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	82.40	gold quality
apex of heart	UBERON:0002098	80.65	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.34	gold quality
sural nerve	UBERON:0015488	77.31	gold quality
granulocyte	CL:0000094	75.86	gold quality
ganglionic eminence	UBERON:0004023	75.09	gold quality
ventricular zone	UBERON:0003053	74.97	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	74.42	gold quality
right atrium auricular region	UBERON:0006631	73.90	gold quality
heart left ventricle	UBERON:0002084	73.64	gold quality
amygdala	UBERON:0001876	73.62	gold quality
temporal lobe	UBERON:0001871	73.56	gold quality
Ammon’s horn	UBERON:0001954	73.56	gold quality
prefrontal cortex	UBERON:0000451	73.52	gold quality
skeletal muscle tissue	UBERON:0001134	73.30	gold quality
substantia nigra	UBERON:0002038	72.99	gold quality
frontal cortex	UBERON:0001870	72.73	gold quality
heart	UBERON:0000948	72.70	gold quality
colonic epithelium	UBERON:0000397	72.63	gold quality
primary visual cortex	UBERON:0002436	72.37	gold quality
fundus of stomach	UBERON:0001160	72.00	gold quality
right lobe of thyroid gland	UBERON:0001119	71.92	gold quality
cerebral cortex	UBERON:0000956	71.84	gold quality
right frontal lobe	UBERON:0002810	71.83	gold quality
putamen	UBERON:0001874	71.82	gold quality
gastrocnemius	UBERON:0001388	71.71	gold quality
muscle tissue	UBERON:0002385	71.63	gold quality
lower esophagus muscularis layer	UBERON:0035833	71.52	gold quality
mucosa of stomach	UBERON:0001199	71.49	gold quality
muscle of leg	UBERON:0001383	71.49	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.09

Regulation

Is transcription factor: no

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), NUTM2B (ENSG00000188199), NUTM2E (ENSG00000228570)

Protein

Protein identifiers

NUT family member 2D — Q5VT03 (reviewed: Q5VT03)

All UniProt accessions (3): Q5VT03, A0A075B6P9, U3KPT3

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the NUT family.

RefSeq proteins (2): NP_001009610, NP_001369233* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR024309	NUT_N	Domain
IPR024310	NUT	Family

Pfam: PF12881

UniProt features (9 total): region of interest 4, compositionally biased region 4, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5VT03-F1	48.45	0.05

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 3 (showing top): chr10q23, BLANCO_MELO_MERS_COV_INFECTION_MCR5_CELLS_UP, PULVER_FOREY_CELLCYCLE_PEAKING_G2_M

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

382 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NUTM2D	FAM25A	B3EWG3	528
NUTM2D	Q8WV35	Q8WV35	480
NUTM2D	B3GNT9	Q6UX72	479
NUTM2D	TOGARAM2	Q6ZUX3	448
NUTM2D	FNDC4	Q9H6D8	397
NUTM2D	CES4A	Q5XG92	389
NUTM2D	PSD2	Q9BQI7	370
NUTM2D	SLC9A5	Q14940	355
NUTM2D	RBKS	Q9H477	352
NUTM2D	MMRN2	Q9H8L6	348
NUTM2D	YPEL5	P62699	348
NUTM2D	CAPN14	A8MX76	335
NUTM2D	ANKRD22	Q5VYY1	324
NUTM2D	NDUFC1	O43677	324
NUTM2D	GPAT2	Q6NUI2	323

IntAct

0 interactions, top by confidence:

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

Cancer significance

From intOGen — cancer-driver classification: activating (oncogene-like) across 1 cancer types — NPC.

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

1187 predictions. Top by Δscore:

Variant	Effect	Δscore
10:87363136:A:AG	acceptor_gain	1.0000
10:87363137:G:GT	acceptor_gain	1.0000
10:87363137:GC:G	acceptor_gain	1.0000
10:87363137:GCC:G	acceptor_gain	1.0000
10:87363137:GCCC:G	acceptor_gain	1.0000
10:87363137:GCCCA:G	acceptor_gain	1.0000
10:87363262:GAAAA:G	donor_gain	1.0000
10:87363263:AAAA:A	donor_gain	1.0000
10:87363264:AAA:A	donor_gain	1.0000
10:87363265:AA:A	donor_gain	1.0000
10:87363266:AG:A	donor_loss	1.0000
10:87363267:G:C	donor_loss	1.0000
10:87363267:G:GG	donor_gain	1.0000
10:87364235:CCAG:C	acceptor_loss	1.0000
10:87364236:CAG:C	acceptor_loss	1.0000
10:87364237:AGG:A	acceptor_loss	1.0000
10:87364820:GT:G	acceptor_gain	1.0000
10:87365680:T:TA	acceptor_gain	1.0000
10:87365685:CCA:C	acceptor_loss	1.0000
10:87365686:CA:C	acceptor_loss	1.0000
10:87365687:A:AG	acceptor_gain	1.0000
10:87365687:A:T	acceptor_loss	1.0000
10:87365687:AG:A	acceptor_gain	1.0000
10:87365687:AGGT:A	acceptor_gain	1.0000
10:87365687:AGGTG:A	acceptor_gain	1.0000
10:87365688:G:GA	acceptor_gain	1.0000
10:87365688:GG:G	acceptor_gain	1.0000
10:87365688:GGT:G	acceptor_gain	1.0000
10:87365688:GGTG:G	acceptor_gain	1.0000
10:87365688:GGTGG:G	acceptor_gain	1.0000

AlphaMissense

5147 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:87361173:T:C	F287L	0.989
10:87361175:C:A	F287L	0.989
10:87361175:C:G	F287L	0.989
10:87363216:G:C	W315C	0.989
10:87363216:G:T	W315C	0.989
10:87363214:T:A	W315R	0.985
10:87363214:T:C	W315R	0.985
10:87363247:T:C	F326L	0.985
10:87363249:C:A	F326L	0.985
10:87363249:C:G	F326L	0.985
10:87364240:T:C	F333L	0.984
10:87364242:C:A	F333L	0.984
10:87364242:C:G	F333L	0.984
10:87364249:T:C	F336L	0.979
10:87364251:T:A	F336L	0.979
10:87364251:T:G	F336L	0.979
10:87363239:G:C	R323P	0.971
10:87365713:T:C	F515L	0.967
10:87365715:C:A	F515L	0.967
10:87365715:C:G	F515L	0.967
10:87363215:G:C	W315S	0.966
10:87363232:T:C	F321L	0.966
10:87363234:T:A	F321L	0.966
10:87363234:T:G	F321L	0.966
10:87364241:T:C	F333S	0.966
10:87361104:T:A	W264R	0.965
10:87361104:T:C	W264R	0.965
10:87361170:T:C	C286R	0.962
10:87361095:T:C	F261L	0.961
10:87361097:C:A	F261L	0.961

dbSNP variants (sampled 300 via entrez): RS1000000514 (10:87369855 C>A,T), RS1001600261 (10:87371019 A>G), RS1003683185 (10:87358579 G>C), RS1004243188 (10:87361200 T>TG), RS1005831300 (10:87357036 G>C), RS1006168657 (10:87367585 C>G), RS1006240743 (10:87368044 C>G,T), RS1007840837 (10:87369914 A>G), RS1008623380 (10:87355960 G>A), RS1009158699 (10:87356672 T>C,G), RS1010240098 (10:87371044 C>A,T), RS1010657929 (10:87355786 G>A), RS1012334154 (10:87365711 A>C), RS1012386665 (10:87362597 T>TA), RS1012718770 (10:87369605 C>G)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

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

11 total (human), top 11 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
ferrous chloride	decreases expression	1
perfluoro-n-nonanoic acid	increases expression	1
perfluorohexanesulfonic acid	increases expression	1
jinfukang	affects cotreatment, decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Cisplatin	affects cotreatment, decreases expression	1
Plant Extracts	decreases expression, affects cotreatment	1
Silicon Dioxide	increases expression	1
Urethane	increases expression	1
Acrylamide	increases expression	1

Clinical trials (associated diseases)

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