NUTM2F

Summary

NUTM2F (NUT family member 2F, HGNC:23450) is a protein-coding gene on chromosome 9q22.32, encoding NUT family member 2F (A1L443).

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 155 total
• MANE Select transcript: NM_017561

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23450
Approved symbol	NUTM2F
Name	NUT family member 2F
Location	9q22.32
Locus type	gene with protein product
Status	Approved
Aliases	DKFZp434I1117
Ensembl gene	ENSG00000130950
Ensembl biotype	protein_coding
Entrez	54754

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000253262

RefSeq mRNA: 1 — MANE Select: NM_017561 NM_017561

CCDS: CCDS47994

Canonical transcript exons

ENST00000253262 — 7 exons

Exon	Start	End
ENSE00000895716	94320208	94320593
ENSE00001536421	94328608	94328644
ENSE00001674698	94325238	94325934
ENSE00001737855	94322201	94322329
ENSE00001750291	94321093	94321232
ENSE00001763885	94319613	94319729
ENSE00003890467	94318198	94319250

Expression profiles

Bgee: expression breadth broad, 13 present calls, max score 50.32.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	50.32	gold quality
testis	UBERON:0000473	49.66	gold quality
right testis	UBERON:0004534	49.35	gold quality
colonic epithelium	UBERON:0000397	45.29	gold quality
bone marrow cell	CL:0002092	45.22	gold quality
cortical plate	UBERON:0005343	43.39	gold quality
ganglionic eminence	UBERON:0004023	40.70	gold quality
lower esophagus mucosa	UBERON:0035834	39.51	gold quality
granulocyte	CL:0000094	37.41	gold quality
kidney	UBERON:0002113	36.91	silver quality
placenta	UBERON:0001987	36.79	silver quality
tonsil	UBERON:0002372	36.56	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
bone marrow	UBERON:0002371	36.37	gold quality
hindlimb stylopod muscle	UBERON:0004252	35.97	gold quality
calcaneal tendon	UBERON:0003701	35.74	gold quality
adult mammalian kidney	UBERON:0000082	35.47	silver quality
blood	UBERON:0000178	35.11	silver quality
cortex of kidney	UBERON:0001225	34.50	silver quality
duodenum	UBERON:0002114	32.48	gold quality
urinary bladder	UBERON:0001255	32.46	silver quality
leukocyte	CL:0000738	32.11	gold quality
uterine cervix	UBERON:0000002	31.97	gold quality
monocyte	CL:0000576	31.92	gold quality
body of pancreas	UBERON:0001150	31.79	silver quality
olfactory segment of nasal mucosa	UBERON:0005386	31.66	gold quality
pancreas	UBERON:0001264	30.95	silver quality
ascending aorta	UBERON:0001496	30.34	gold quality
endocervix	UBERON:0000458	29.99	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.78

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

10 targeting NUTM2F, 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-3941	99.86	70.54	2735
HSA-MIR-383-3P	99.85	65.84	1359
HSA-MIR-765	99.84	68.24	2442
HSA-MIR-11181-3P	99.75	66.38	2205
HSA-MIR-4260	98.78	65.37	848
HSA-MIR-6810-5P	98.29	66.21	975
HSA-MIR-450A-2-3P	97.91	67.56	1459
HSA-MIR-1225-3P	97.29	64.60	876
HSA-MIR-4286	97.20	64.37	1587
HSA-MIR-1913	97.07	66.20	1417

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Nutm2	ENSMUSG00000071909
rattus_norvegicus	Nutm2	ENSRNOG00000027311

Paralogs (6): NUTM1 (ENSG00000184507), NUTM2A (ENSG00000184923), NUTM2G (ENSG00000188152), NUTM2B (ENSG00000188199), NUTM2D (ENSG00000214562), NUTM2E (ENSG00000228570)

Protein

Protein identifiers

NUT family member 2F — A1L443 (reviewed: A1L443)

All UniProt accessions (1): A1L443

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the NUT family.

RefSeq proteins (1): NP_060031* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR024309	NUT_N	Domain
IPR024310	NUT	Family

Pfam: PF12881

UniProt features (15 total): compositionally biased region 5, region of interest 4, sequence conflict 3, sequence variant 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A1L443-F1	52.27	0.13

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 13 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_DN, MODULE_255, MODULE_317, chr9q22, MODULE_69, SENGUPTA_EBNA1_ANTICORRELATED, MODULE_37, MODULE_532, MODULE_459, MODULE_179, MODULE_378, MODULE_136, GSE34156_UNTREATED_VS_24H_NOD2_AND_TLR1_TLR2_LIGAND_TREATED_MONOCYTE_DN

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

470 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NUTM2F	SPDYE1	Q8NFV5	627
NUTM2F	ZBED8L	Q8TCP9	571
NUTM2F	ERICH6B	Q5W0A0	510
NUTM2F	B9ZVM9	B9ZVM9	507
NUTM2F	DIP2C-AS1	Q8N8Z3	507
NUTM2F	OR2T34	Q8NGX1	507
NUTM2F	ZNF169	Q14929	448
NUTM2F	ZNF510	Q9Y2H8	447
NUTM2F	FAM9B	Q8IZU0	431
NUTM2F	RWDD3	Q9Y3V2	398
NUTM2F	DUS3L	Q96G46	396
NUTM2F	NOL11	Q9H8H0	385
NUTM2F	ASB16	Q96NS5	372
NUTM2F	TAS2R43	P59537	359
NUTM2F	OR2T27	Q8NH04	354

IntAct

3 interactions, top by confidence:

A	B	Type	Score
ZNF148	NUTM2F	psi-mi:“MI:0915”(physical association)	0.370
NUTM2F	IRF6	psi-mi:“MI:0914”(association)	0.350

BioGRID (48): NUTM2F (Two-hybrid), NUTM2F (Two-hybrid), MORN4 (Two-hybrid), NUTM2F (Two-hybrid), NUTM2F (Two-hybrid), NUTM2F (Two-hybrid), NUTM2F (Two-hybrid), NUTM2F (Two-hybrid), NUTM2F (Two-hybrid), OSTF1 (Two-hybrid), SH3GL1 (Two-hybrid), SH3RF1 (Two-hybrid), RBM47 (Two-hybrid), ZNF148 (Two-hybrid), PRPF18 (Two-hybrid)

ESM2 similar proteins: A0A0J9YX94, A0A0J9YXQ4, A0A0J9YY54, A0A494C1R9, A1L443, A5D7L8, A6NDY0, A6NKD2, E9PGG2, F6SZT2, O19110, O75807, O88852, P0CV98, P0CV99, P0CW00, P0CW01, P0CW24, P0DV79, P17564, P59644, P78358, Q01534, Q0P5N2, Q15735, Q2KI51, Q587J8, Q5R5G8, Q5R6R8, Q5RFC2, Q5SV97, Q60465, Q6P752, Q86V59, Q8BSI6, Q8N9W4, Q8NAG6, Q8NEE8, Q8VD63, Q95LS7

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

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	139
Likely benign	16
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1297 predictions. Top by Δscore:

Variant	Effect	Δscore
9:94319607:CTCTA:C	donor_loss	1.0000
9:94319609:CTA:C	donor_loss	1.0000
9:94319610:TACCT:T	donor_loss	1.0000
9:94319611:ACCTG:A	donor_loss	1.0000
9:94319632:T:TA	donor_gain	1.0000
9:94319635:T:TA	donor_gain	1.0000
9:94319725:TCCAC:T	acceptor_gain	1.0000
9:94319726:CCAC:C	acceptor_gain	1.0000
9:94319726:CCACC:C	acceptor_gain	1.0000
9:94319727:CAC:C	acceptor_gain	1.0000
9:94319727:CACC:C	acceptor_gain	1.0000
9:94319728:AC:A	acceptor_gain	1.0000
9:94319729:CC:C	acceptor_gain	1.0000
9:94319730:C:CC	acceptor_gain	1.0000
9:94319730:CTG:C	acceptor_loss	1.0000
9:94319731:T:A	acceptor_loss	1.0000
9:94319737:C:CT	acceptor_gain	1.0000
9:94319738:A:T	acceptor_gain	1.0000
9:94320204:CCA:C	donor_loss	1.0000
9:94320205:CA:C	donor_loss	1.0000
9:94320207:CC:C	donor_loss	1.0000
9:94320224:T:TA	donor_gain	1.0000
9:94321231:ACCTG:A	acceptor_loss	1.0000
9:94322197:TCAC:T	donor_loss	1.0000
9:94322198:CAC:C	donor_loss	1.0000
9:94322199:A:AC	donor_gain	1.0000
9:94322200:C:CG	donor_gain	1.0000
9:94322200:CT:C	donor_gain	1.0000
9:94322200:CTT:C	donor_gain	1.0000
9:94322200:CTTT:C	donor_gain	1.0000

AlphaMissense

4828 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:94321229:G:C	F282L	0.980
9:94321229:G:T	F282L	0.980
9:94321231:A:G	F282L	0.980
9:94322251:C:A	W264C	0.980
9:94322251:C:G	W264C	0.980
9:94325243:G:C	F236L	0.976
9:94325243:G:T	F236L	0.976
9:94325245:A:G	F236L	0.976
9:94322253:A:G	W264R	0.975
9:94322253:A:T	W264R	0.975
9:94319703:G:C	F465L	0.971
9:94319703:G:T	F465L	0.971
9:94319705:A:G	F465L	0.971
9:94321220:A:C	F285L	0.971
9:94321220:A:T	F285L	0.971
9:94321222:A:G	F285L	0.971
9:94322218:G:C	F275L	0.968
9:94322218:G:T	F275L	0.968
9:94322220:A:G	F275L	0.968
9:94321230:A:G	F282S	0.962
9:94322228:C:G	R272P	0.962
9:94319704:A:G	F465S	0.961
9:94320217:A:C	F453L	0.954
9:94320217:A:T	F453L	0.954
9:94320219:A:G	F453L	0.954
9:94325321:G:C	F210L	0.953
9:94325321:G:T	F210L	0.953
9:94325323:A:G	F210L	0.953
9:94325314:A:G	W213R	0.952
9:94325314:A:T	W213R	0.952

dbSNP variants (sampled 300 via entrez): RS1000016172 (9:94319794 C>A,G,T), RS1000311776 (9:94321793 C>T), RS1000414513 (9:94327228 T>A,C), RS1000487877 (9:94326781 T>C), RS1000825275 (9:94325287 T>C), RS1001051285 (9:94320790 C>G,T), RS1001705613 (9:94322399 C>G,T), RS1002121615 (9:94321205 C>T), RS1002174467 (9:94326351 GGAAACCA>G), RS1002665406 (9:94326012 C>T), RS1002708461 (9:94323648 G>C), RS1003329207 (9:94329844 G>A), RS1003636492 (9:94328221 C>T), RS1004295845 (9:94326389 T>A,C), RS1004535393 (9:94321720 T>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

3 associations (top):

Study	Trait	p-value
GCST004482_27	Peripheral arterial disease (traffic-related air pollution interaction)	7.000000e-08
GCST004904_63	Body mass index	2.000000e-09
GCST90000025_406	Appendicular lean mass	9.000000e-13

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0007908	traffic air pollution measurement
EFO:0004340	body mass index
EFO:0004980	appendicular lean mass

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

9 total (human), top 9 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects expression	1
butyraldehyde	increases expression	1
tebuconazole	decreases expression	1
CGP 52608	affects binding, increases reaction	1
abrine	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Particulate Matter	increases abundance, increases expression	1

Clinical trials (associated diseases)

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