NUTM2E

Summary

NUTM2E (NUT family member 2E, HGNC:23448) is a protein-coding gene on chromosome 10q22.3, encoding NUT family member 2E (B1AL46).

At a glance

• Clinical variants (ClinVar): 6 total
• MANE Select transcript: NM_001355263

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23448
Approved symbol	NUTM2E
Name	NUT family member 2E
Location	10q22.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000228570
Ensembl biotype	protein_coding
Entrez	283008

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000429984, ENST00000602967

RefSeq mRNA: 1 — MANE Select: NM_001355263 NM_001355263

CCDS: CCDS91285

Canonical transcript exons

ENST00000429984 — 10 exons

Exon	Start	End
ENSE00002441976	79848513	79848895
ENSE00002450251	79849821	79850878
ENSE00002467773	79846830	79846958
ENSE00002483375	79849371	79849487
ENSE00002498825	79844173	79844872
ENSE00002517775	79847931	79848070
ENSE00003918438	79826739	79827357
ENSE00003918568	79839628	79842122
ENSE00003920477	79838309	79838586
ENSE00003920727	79838780	79839115

Expression profiles

Bgee: expression breadth ubiquitous, 119 present calls, max score 60.77.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
bone marrow cell	CL:0002092	60.77	silver quality
stromal cell of endometrium	CL:0002255	60.55	gold quality
apex of heart	UBERON:0002098	57.04	gold quality
primary visual cortex	UBERON:0002436	55.24	gold quality
right uterine tube	UBERON:0001302	53.05	gold quality
ventricular zone	UBERON:0003053	52.04	gold quality
colonic epithelium	UBERON:0000397	51.22	gold quality
blood	UBERON:0000178	50.06	gold quality
prefrontal cortex	UBERON:0000451	49.86	gold quality
tonsil	UBERON:0002372	48.61	silver quality
islet of Langerhans	UBERON:0000006	48.01	gold quality
muscle tissue	UBERON:0002385	47.07	gold quality
cortical plate	UBERON:0005343	46.72	gold quality
skeletal muscle tissue	UBERON:0001134	46.56	gold quality
lymph node	UBERON:0000029	46.41	gold quality
fundus of stomach	UBERON:0001160	46.02	gold quality
smooth muscle tissue	UBERON:0001135	45.95	gold quality
superior frontal gyrus	UBERON:0002661	45.76	gold quality
frontal cortex	UBERON:0001870	45.55	gold quality
granulocyte	CL:0000094	45.20	silver quality
olfactory segment of nasal mucosa	UBERON:0005386	45.12	gold quality
pancreas	UBERON:0001264	45.10	gold quality
monocyte	CL:0000576	44.57	silver quality
ganglionic eminence	UBERON:0004023	44.27	gold quality
duodenum	UBERON:0002114	44.20	gold quality
liver	UBERON:0002107	44.18	silver quality
cerebellum	UBERON:0002037	44.06	gold quality
adenohypophysis	UBERON:0002196	43.94	gold quality
leukocyte	CL:0000738	43.89	silver quality
cerebellar cortex	UBERON:0002129	43.85	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.34

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• 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)

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), NUTM2D (ENSG00000214562)

Protein

Protein identifiers

NUT family member 2E — B1AL46 (reviewed: B1AL46)

All UniProt accessions (2): B1AL46, R4GNA6

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the NUT family.

RefSeq proteins (1): NP_001342192* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR024309	NUT_N	Domain
IPR024310	NUT	Family

Pfam: PF12881

UniProt features (10 total): region of interest 5, compositionally biased region 4, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-B1AL46-F1	47.81	0.08

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 4 (showing top): GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_DN, JINESH_BLEBBISHIELD_VS_LIVE_CONTROL_UP, JINESH_BLEBBISHIELD_TRANSFORMED_STEM_CELL_SPHERES_DN, chr10q22

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

372 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NUTM2E	YWHAE	P29360	518
NUTM2E	ZC3H7B	Q9UGR2	461
NUTM2E	CCNB3	Q8WWL7	401
NUTM2E	BRD8	Q9H0E9	314
NUTM2E	PHF1	O43189	309
NUTM2E	PHF21A	Q96BD5	309
NUTM2E	LRP12	Q9Y561	306
NUTM2E	NOTCH2NLA	Q7Z3S9	278
NUTM2E	RNF111	Q6ZNA4	278
NUTM2E	BCORL1	Q5H9F3	269
NUTM2E	JAZF1	Q86VZ6	254
NUTM2E	FBXO25	Q8TCJ0	253
NUTM2E	KAT6B	Q8WYB5	244
NUTM2E	MEAF6	Q9HAF1	236
NUTM2E	IRX2	Q9BZI1	234

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

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	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1225 predictions. Top by Δscore:

Variant	Effect	Δscore
10:79846828:A:AG	acceptor_gain	1.0000
10:79846829:G:GT	acceptor_gain	1.0000
10:79846829:GC:G	acceptor_gain	1.0000
10:79846829:GCC:G	acceptor_gain	1.0000
10:79846829:GCCC:G	acceptor_gain	1.0000
10:79846829:GCCCA:G	acceptor_gain	1.0000
10:79846954:GAAAA:G	donor_gain	1.0000
10:79846955:AAAA:A	donor_gain	1.0000
10:79846956:AAA:A	donor_gain	1.0000
10:79846957:AA:A	donor_gain	1.0000
10:79846957:AAGT:A	donor_loss	1.0000
10:79846958:AGT:A	donor_loss	1.0000
10:79846959:G:GG	donor_gain	1.0000
10:79848512:GT:G	acceptor_gain	1.0000
10:79848891:CCAAG:C	donor_loss	1.0000
10:79848892:CAAG:C	donor_loss	1.0000
10:79848893:AAG:A	donor_loss	1.0000
10:79848894:AGGT:A	donor_loss	1.0000
10:79848895:GGT:G	donor_loss	1.0000
10:79848896:G:C	donor_loss	1.0000
10:79849362:T:A	acceptor_gain	1.0000
10:79849367:CCAG:C	acceptor_loss	1.0000
10:79849368:CAGGT:C	acceptor_loss	1.0000
10:79849369:A:AG	acceptor_gain	1.0000
10:79849369:AG:A	acceptor_gain	1.0000
10:79849369:AGGT:A	acceptor_gain	1.0000
10:79849369:AGGTG:A	acceptor_gain	1.0000
10:79849370:G:GA	acceptor_gain	1.0000
10:79849370:GG:G	acceptor_gain	1.0000
10:79849370:GGT:G	acceptor_gain	1.0000

AlphaMissense

5614 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:79847932:T:C	F405L	0.989
10:79847934:C:A	F405L	0.989
10:79847934:C:G	F405L	0.989
10:79847941:T:C	F408L	0.988
10:79847943:T:A	F408L	0.988
10:79847943:T:G	F408L	0.988
10:79844865:T:C	F359L	0.987
10:79844867:C:A	F359L	0.987
10:79844867:C:G	F359L	0.987
10:79846908:G:C	W387C	0.985
10:79846908:G:T	W387C	0.985
10:79846906:T:A	W387R	0.983
10:79846906:T:C	W387R	0.983
10:79847933:T:C	F405S	0.980
10:79844796:T:A	W336R	0.979
10:79844796:T:C	W336R	0.979
10:79846939:T:C	F398L	0.979
10:79846941:C:A	F398L	0.979
10:79846941:C:G	F398L	0.979
10:79844787:T:C	F333L	0.978
10:79844789:C:A	F333L	0.978
10:79844789:C:G	F333L	0.978
10:79844798:G:C	W336C	0.975
10:79844798:G:T	W336C	0.975
10:79849395:T:C	F587L	0.973
10:79849397:C:A	F587L	0.973
10:79849397:C:G	F587L	0.973
10:79844810:G:C	K340N	0.972
10:79844810:G:T	K340N	0.972
10:79844818:C:A	A343D	0.971

dbSNP variants (sampled 300 via entrez): RS1000236357 (10:79825863 A>G), RS1000630059 (10:79839115 G>A), RS1000670512 (10:79826039 C>A,G,T), RS1000756928 (10:79832286 T>G), RS1001002094 (10:79838943 G>A), RS1001298151 (10:79835936 G>T), RS1001351323 (10:79828546 G>A), RS1001423575 (10:79829173 A>G), RS1001946692 (10:79825058 G>A), RS1002268837 (10:79837312 C>G), RS1002357792 (10:79830201 G>A), RS1002375147 (10:79837984 G>A), RS1002429785 (10:79830425 G>T), RS1002708023 (10:79837689 C>G), RS1002869104 (10:79845699 A>C)

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

5 total (human), top 5 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
2,3,5-trichloro-6-phenyl-(1,4)benzoquinone	increases expression	1
Leflunomide	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Acrylamide	increases expression	1

Clinical trials (associated diseases)

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