OR4M2-OT1

Summary

OR4M2-OT1 (OR4M2 overlapping transcript 1, HGNC:56199) is a protein-coding gene on chromosome 15q11.2.

At a glance

• Clinical variants (ClinVar): 8 total

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:56199
Approved symbol	OR4M2-OT1
Name	OR4M2 overlapping transcript 1
Location	15q11.2
Locus type	RNA, long non-coding
Status	Approved
Ensembl gene	ENSG00000285472
Ensembl biotype	protein_coding
Entrez	101927079
RNAcentral	URS0002A146AA — lncRNA, 1370 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000639059

RefSeq mRNA: 0 — MANE Select: None

CCDS: CCDS32173

Canonical transcript exons

ENST00000639059 — 7 exons

Exon	Start	End
ENSE00003801742	22094513	22095857
ENSE00003803712	22058721	22058816
ENSE00003807009	22015233	22015331
ENSE00003808910	22059632	22059835
ENSE00003810853	22044437	22044825
ENSE00003816883	22030926	22031020
ENSE00003822300	22059321	22059409

Expression profiles

Bgee: expression breadth tissue_specific, 7 present calls, max score 78.86.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.86	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	56.61	silver quality
left testis	UBERON:0004533	54.31	gold quality
testis	UBERON:0000473	54.22	gold quality
right testis	UBERON:0004534	53.48	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
bone marrow	UBERON:0002371	31.74	gold quality
muscle tissue	UBERON:0002385	31.06	gold quality
sural nerve	UBERON:0015488	30.93	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
prefrontal cortex	UBERON:0000451	29.04	gold quality
liver	UBERON:0002107	28.28	gold quality
duodenum	UBERON:0002114	28.14	gold quality
lymph node	UBERON:0000029	27.57	gold quality
tonsil	UBERON:0002372	27.05	gold quality
leukocyte	CL:0000738	26.58	gold quality
islet of Langerhans	UBERON:0000006	26.55	gold quality
monocyte	CL:0000576	26.48	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality
blood	UBERON:0000178	26.00	gold quality
gall bladder	UBERON:0002110	25.98	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	25.89	gold quality
placenta	UBERON:0001987	25.81	gold quality
urinary bladder	UBERON:0001255	25.72	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.27

Regulation

Is transcription factor: no

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Canonical reviewed UniProt: None (reviewed: )

All UniProt accessions (1): A0A126GVN2

RefSeq proteins (0): (*=MANE)

Domains & families (InterPro)

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 1 (showing top): chr15q11

GO Biological Process (4): signal transduction (GO:0007165), G protein-coupled receptor signaling pathway (GO:0007186), sensory perception of smell (GO:0007608), detection of chemical stimulus involved in sensory perception of smell (GO:0050911)

GO Molecular Function (2): G protein-coupled receptor activity (GO:0004930), olfactory receptor activity (GO:0004984)

GO Cellular Component (2): plasma membrane (GO:0005886), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transmembrane signaling receptor activity	2
cell communication	1
cellular process	1
signaling	1
regulation of cellular process	1
cellular response to stimulus	1
G protein-coupled receptor activity	1
signal transduction	1
sensory perception of chemical stimulus	1
sensory perception of smell	1
detection of chemical stimulus involved in sensory perception	1
G protein-coupled receptor signaling pathway	1
detection of chemical stimulus involved in sensory perception of smell	1
membrane	1
cell periphery	1
cellular anatomical structure	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

0 interactions, top by confidence:

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	8
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

414 predictions. Top by Δscore:

Variant	Effect	Δscore
15:22095217:G:T	donor_gain	0.9900
15:22095349:A:AG	acceptor_gain	0.8800
15:22095350:G:GG	acceptor_gain	0.8800
15:22080692:TCC:T	donor_gain	0.8700
15:22095028:T:TA	acceptor_gain	0.8500
15:22095347:ACAGT:A	acceptor_gain	0.8400
15:22080746:G:GT	donor_gain	0.8300
15:22095217:G:GT	donor_gain	0.8300
15:22095349:AGT:A	acceptor_gain	0.7900
15:22095350:GTG:G	acceptor_gain	0.7900
15:22095350:GT:G	acceptor_gain	0.7800
15:22094544:T:TA	donor_gain	0.7600
15:22094545:A:AA	donor_gain	0.7600
15:22080651:GAC:G	donor_gain	0.7400
15:22080652:ACA:A	donor_gain	0.7400
15:22095346:C:G	acceptor_gain	0.7300
15:22080653:C:G	donor_gain	0.7200
15:22080693:C:A	donor_gain	0.7000
15:22080747:A:T	donor_gain	0.7000
15:22095348:C:G	acceptor_gain	0.7000
15:22094586:A:G	donor_gain	0.6900
15:22095350:GTGAT:G	acceptor_gain	0.6700
15:22080855:A:AG	acceptor_gain	0.6600
15:22080856:G:GG	acceptor_gain	0.6600
15:22095233:TCC:T	donor_gain	0.6500
15:22095237:C:G	donor_gain	0.6400
15:22095255:T:G	donor_gain	0.6400
15:22080945:T:A	acceptor_gain	0.6300
15:22095253:C:A	donor_gain	0.6100
15:22095345:A:AG	acceptor_gain	0.6100

AlphaMissense

2086 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:22094555:T:C	F12L	0.856
15:22094557:T:A	F12L	0.856
15:22094557:T:G	F12L	0.856
15:22095023:T:C	F168L	0.840
15:22095025:T:A	F168L	0.840
15:22095025:T:G	F168L	0.840
15:22095272:T:C	F251L	0.780
15:22095274:T:A	F251L	0.780
15:22095274:T:G	F251L	0.780
15:22095050:T:C	F177L	0.763
15:22095052:C:A	F177L	0.763
15:22095052:C:G	F177L	0.763
15:22094603:T:C	F28L	0.741
15:22094605:T:A	F28L	0.741
15:22094605:T:G	F28L	0.741
15:22094825:T:C	F102L	0.716
15:22094827:T:A	F102L	0.716
15:22094827:T:G	F102L	0.716
15:22095305:T:C	F262L	0.715
15:22095307:C:A	F262L	0.715
15:22095307:C:G	F262L	0.715
15:22095053:T:C	F178L	0.705
15:22095055:C:A	F178L	0.705
15:22095055:C:G	F178L	0.705
15:22095152:T:C	F211L	0.663
15:22095154:T:A	F211L	0.663
15:22095154:T:G	F211L	0.663
15:22094556:T:C	F12S	0.652
15:22095356:T:C	F279L	0.649
15:22095358:T:A	F279L	0.649

dbSNP variants (sampled 300 via entrez): RS1000136038 (15:22014626 T>A), RS1000174732 (15:22084006 T>A,C), RS1000579112 (15:20991941 C>G), RS1000778575 (15:22088136 A>G), RS1000863862 (15:20992421 T>G), RS1001152220 (15:22019847 C>T), RS1001470560 (15:20999449 A>G), RS1001473945 (15:22042474 G>A), RS1001738120 (15:22041384 T>C), RS1001818029 (15:20996963 A>G), RS1002158003 (15:22024617 T>C), RS1002188993 (15:22023491 G>A), RS1002404410 (15:20977622 T>C), RS1002512383 (15:22075080 G>T), RS1003225305 (15:22094491 C>T)

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: 0 entries

Clinical trials (associated diseases)

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