LSMEM2

Summary

LSMEM2 (leucine rich single-pass membrane protein 2, HGNC:26781) is a protein-coding gene on chromosome 3p21.31, encoding Leucine-rich single-pass membrane protein 2 (Q8N112).

Predicted to be located in membrane.

Source: NCBI Gene 132228 — RefSeq curated summary.

At a glance

• GWAS associations: 10
• Clinical variants (ClinVar): 38 total
• MANE Select transcript: NM_153215

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26781
Approved symbol	LSMEM2
Name	leucine rich single-pass membrane protein 2
Location	3p21.31
Locus type	gene with protein product
Status	Approved
Aliases	FLJ38608
Ensembl gene	ENSG00000179564
Ensembl biotype	protein_coding
OMIM	621358
Entrez	132228

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000316436, ENST00000878856, ENST00000948602, ENST00000948603

RefSeq mRNA: 2 — MANE Select: NM_153215 NM_001304385, NM_153215

CCDS: CCDS2814

Canonical transcript exons

ENST00000316436 — 4 exons

Exon	Start	End
ENSE00001275321	50286674	50286862
ENSE00001275330	50286471	50286584
ENSE00001275338	50287069	50288114
ENSE00001275343	50279087	50279171

Expression profiles

Bgee: expression breadth ubiquitous, 149 present calls, max score 89.81.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1506 / max 35.3219, expressed in 39 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
36724	0.0731	25
36725	0.0423	21
36723	0.0352	16

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
apex of heart	UBERON:0002098	89.81	gold quality
heart left ventricle	UBERON:0002084	84.08	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.61	gold quality
cardiac ventricle	UBERON:0002082	83.39	gold quality
hindlimb stylopod muscle	UBERON:0004252	81.00	gold quality
right atrium auricular region	UBERON:0006631	77.47	gold quality
heart	UBERON:0000948	77.33	gold quality
left ventricle myocardium	UBERON:0006566	75.91	gold quality
cardiac atrium	UBERON:0002081	75.62	gold quality
muscle of leg	UBERON:0001383	75.19	gold quality
gastrocnemius	UBERON:0001388	74.34	gold quality
buccal mucosa cell	CL:0002336	73.55	gold quality
skeletal muscle tissue	UBERON:0001134	72.66	gold quality
heart right ventricle	UBERON:0002080	72.22	silver quality
tibial nerve	UBERON:0001323	71.71	gold quality
muscle tissue	UBERON:0002385	69.46	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	68.99	gold quality
tendon of biceps brachii	UBERON:0008188	67.44	gold quality
right testis	UBERON:0004534	65.57	gold quality
left testis	UBERON:0004533	65.21	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	64.81	gold quality
testis	UBERON:0000473	63.13	gold quality
putamen	UBERON:0001874	62.84	gold quality
spinal cord	UBERON:0002240	62.63	gold quality
parotid gland	UBERON:0001831	62.32	gold quality
endocervix	UBERON:0000458	61.61	gold quality
left uterine tube	UBERON:0001303	60.02	gold quality
caudate nucleus	UBERON:0001873	59.38	gold quality
body of uterus	UBERON:0009853	59.28	gold quality
amygdala	UBERON:0001876	58.93	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.22

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

33 targeting LSMEM2, 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-4650-5P	99.98	64.69	999
HSA-MIR-1229-3P	99.97	66.49	906
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-7856-5P	99.75	69.99	2901
HSA-MIR-12124	99.68	69.17	2700
HSA-MIR-9851-3P	99.63	69.68	1110
HSA-MIR-593-5P	99.34	69.50	965
HSA-MIR-4477B	99.23	70.49	1733
HSA-MIR-361-3P	99.19	66.45	1381
HSA-MIR-10399-5P	99.17	69.87	2610
HSA-MIR-6504-3P	99.17	69.31	2891
HSA-MIR-4651	99.06	67.57	2002
HSA-MIR-6830-5P	99.01	68.73	1884
HSA-MIR-608	98.93	67.83	2013
HSA-MIR-4709-3P	98.88	68.04	1594
HSA-MIR-4297	98.77	66.95	2013
HSA-MIR-7114-3P	98.42	66.53	569
HSA-MIR-619-3P	98.38	65.58	693
HSA-MIR-541-5P	98.24	67.77	1181
HSA-MIR-1262	98.17	66.52	757
HSA-MIR-4701-3P	98.17	66.25	788
HSA-MIR-6736-5P	98.17	66.43	760
HSA-MIR-4518	98.12	66.82	1030
HSA-MIR-4421	97.99	64.89	701
HSA-MIR-637	97.91	64.05	1517
HSA-MIR-5699-3P	97.81	65.00	861
HSA-MIR-1266-5P	97.71	66.92	1052
HSA-MIR-6511A-3P	97.60	66.61	713
HSA-MIR-6511B-3P	97.60	66.61	713
HSA-MIR-6773-5P	97.04	64.30	595

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Lsmem2	ENSMUSG00000103409
rattus_norvegicus	Lsmem2	ENSRNOG00000052634

Protein

Protein identifiers

Leucine-rich single-pass membrane protein 2 — Q8N112 (reviewed: Q8N112)

All UniProt accessions (1): Q8N112

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (2): NP_001291314, NP_694947* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031674	DUF4714	Family

Pfam: PF15833

UniProt features (2 total): chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N112-F1	66.93	0.16

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 33 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_DN, RNGTGGGC_UNKNOWN, TGGNNNNNNKCCAR_UNKNOWN, CTAWWWATA_RSRFC4_Q2, MIKKELSEN_IPS_ICP_WITH_H3K27ME3, MARTENS_TRETINOIN_RESPONSE_DN, chr3p21, MIR7856_5P, MIR6504_3P, MIR10399_5P, MIR4477B, MIR608, MIR4651, MIR9851_3P, MIR541_5P

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

196 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LSMEM2	C5orf24	Q7Z6I8	506
LSMEM2	ZNF551	P17034	505
LSMEM2	KLHL34	Q8N239	488
LSMEM2	ADPRHL1	Q8NDY3	485
LSMEM2	WDR47	O94967	484
LSMEM2	TASOR2	Q5VWN6	446
LSMEM2	KLHL23	Q8NBE8	418
LSMEM2	LRRK1	Q38SD2	397
LSMEM2	ARHGAP21	Q5T5U3	388
LSMEM2	IFRD2	Q12894	380
LSMEM2	CWH43	Q9H720	370
LSMEM2	UBAP2	Q5T6F2	360
LSMEM2	SYNPO2L	Q9H987	350
LSMEM2	CAND2	O75155	348
LSMEM2	AP3D1	O14617	346

IntAct

74 interactions, top by confidence:

A	B	Type	Score
STX7	LSMEM2	psi-mi:“MI:0915”(physical association)	0.740
LSMEM2	STX7	psi-mi:“MI:0914”(association)	0.740
LSMEM1	LSMEM2	psi-mi:“MI:0915”(physical association)	0.720
GIMAP5	LSMEM2	psi-mi:“MI:0915”(physical association)	0.720
LSMEM2	LSMEM1	psi-mi:“MI:0915”(physical association)	0.720
LSMEM2	GIMAP5	psi-mi:“MI:0915”(physical association)	0.720
TMEM218	LSMEM2	psi-mi:“MI:0915”(physical association)	0.560
LSMEM2	SEC22A	psi-mi:“MI:0915”(physical association)	0.560
SGTA	LSMEM2	psi-mi:“MI:0915”(physical association)	0.560
LSMEM2	SPG21	psi-mi:“MI:0915”(physical association)	0.560
SFTPC	LSMEM2	psi-mi:“MI:0915”(physical association)	0.560
LSMEM2	SMIM3	psi-mi:“MI:0915”(physical association)	0.560
KLRC1	LSMEM2	psi-mi:“MI:0915”(physical association)	0.560
EMP1	LSMEM2	psi-mi:“MI:0915”(physical association)	0.560
CLEC12B	LSMEM2	psi-mi:“MI:0915”(physical association)	0.560
LSMEM2	TMEM143	psi-mi:“MI:0915”(physical association)	0.560
PLN	LSMEM2	psi-mi:“MI:0915”(physical association)	0.560
CD72	LSMEM2	psi-mi:“MI:0915”(physical association)	0.560
LSMEM2	SPACA1	psi-mi:“MI:0915”(physical association)	0.560
CLDN7	LSMEM2	psi-mi:“MI:0915”(physical association)	0.560
CXCL9	LSMEM2	psi-mi:“MI:0915”(physical association)	0.560
CTXN3	LSMEM2	psi-mi:“MI:0915”(physical association)	0.560
LSMEM2	PCDH17	psi-mi:“MI:0914”(association)	0.350

BioGRID (52): LSMEM2 (Two-hybrid), LSMEM1 (Two-hybrid), LSMEM2 (Two-hybrid), LSMEM2 (Two-hybrid), LSMEM2 (Two-hybrid), LSMEM2 (Two-hybrid), LSMEM2 (Two-hybrid), LSMEM2 (Two-hybrid), LSMEM2 (Two-hybrid), LSMEM2 (Two-hybrid), LSMEM2 (Two-hybrid), LSMEM2 (Two-hybrid), LSMEM2 (Two-hybrid), LSMEM2 (Two-hybrid), LSMEM1 (Two-hybrid)

ESM2 similar proteins: A0A1B0GW64, A0A5F4BST2, A0PJX4, A8MVS5, A8MWV9, B0FP48, E5RIL1, E9PGG2, O14836, O60320, O95998, P09564, Q01113, Q01114, Q13477, Q2KI80, Q2T9R2, Q3TS39, Q3UPR0, Q3URD2, Q4V9L6, Q5FVJ4, Q5M869, Q6A044, Q6UWJ8, Q75VT8, Q864V4, Q8BRJ3, Q8BX43, Q8C503, Q8IVY1, Q8K5A9, Q8N112, Q8NC24, Q8NDY8, Q8QZT4, Q8R138, Q969Z4, Q9BUF7, Q9CQM1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	32
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

411 predictions. Top by Δscore:

Variant	Effect	Δscore
3:50286469:A:AG	acceptor_gain	1.0000
3:50286470:G:GA	acceptor_gain	1.0000
3:50286585:G:GA	donor_loss	1.0000
3:50286586:T:A	donor_loss	1.0000
3:50287066:CA:C	acceptor_loss	1.0000
3:50287067:A:AG	acceptor_gain	1.0000
3:50287067:AGT:A	acceptor_gain	1.0000
3:50287068:G:GT	acceptor_gain	1.0000
3:50287068:GT:G	acceptor_gain	1.0000
3:50287068:GTG:G	acceptor_gain	1.0000
3:50287068:GTGCT:G	acceptor_gain	1.0000
3:50279168:GAAG:G	donor_gain	0.9900
3:50279169:AAGG:A	donor_loss	0.9900
3:50279170:AGG:A	donor_loss	0.9900
3:50279172:G:GA	donor_loss	0.9900
3:50279173:T:A	donor_loss	0.9900
3:50286465:CTGCA:C	acceptor_loss	0.9900
3:50286466:TGCAG:T	acceptor_loss	0.9900
3:50286468:CAGAC:C	acceptor_loss	0.9900
3:50286470:G:T	acceptor_loss	0.9900
3:50286470:GA:G	acceptor_gain	0.9900
3:50286470:GACTC:G	acceptor_gain	0.9900
3:50287061:A:AG	acceptor_gain	0.9900
3:50287065:A:AG	acceptor_gain	0.9900
3:50287065:ACAGT:A	acceptor_gain	0.9900
3:50287066:C:G	acceptor_gain	0.9900
3:50287068:GTGC:G	acceptor_gain	0.9900
3:50286389:A:G	acceptor_gain	0.9800
3:50286470:GAC:G	acceptor_gain	0.9800
3:50286470:GACT:G	acceptor_gain	0.9800

AlphaMissense

1034 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:50286859:A:C	S120R	0.985
3:50286861:C:A	S120R	0.985
3:50286861:C:G	S120R	0.985
3:50286826:T:C	C109R	0.983
3:50287149:A:C	S148R	0.973
3:50287151:C:A	S148R	0.973
3:50287151:C:G	S148R	0.973
3:50286564:T:C	I51T	0.965
3:50287138:T:C	L144P	0.951
3:50286564:T:A	I51N	0.944
3:50286566:A:C	S52R	0.941
3:50286568:C:A	S52R	0.941
3:50286568:C:G	S52R	0.941
3:50286848:C:A	A116D	0.934
3:50286857:T:C	L119P	0.933
3:50286564:T:G	I51S	0.931
3:50287108:T:C	L134P	0.930
3:50286839:C:A	A113E	0.925
3:50286851:T:A	V117D	0.924
3:50287120:A:T	E138V	0.923
3:50286836:T:A	L112H	0.916
3:50286560:T:C	S50P	0.913
3:50287083:T:C	S126P	0.912
3:50286860:G:A	S120N	0.906
3:50286853:T:G	Y118D	0.904
3:50287087:T:C	L127P	0.904
3:50287108:T:A	L134H	0.903
3:50286828:C:G	C109W	0.899
3:50286860:G:T	S120I	0.897
3:50287076:G:C	Q123H	0.896

dbSNP variants (sampled 300 via entrez): RS1000856427 (3:50280716 C>A,T), RS1000908888 (3:50280930 A>C), RS1001583827 (3:50284228 G>A,C), RS1001601310 (3:50276479 G>A,T), RS1001865021 (3:50282613 G>A), RS1001915713 (3:50282994 G>A), RS1002137063 (3:50276717 C>A,G,T), RS1002534420 (3:50285492 T>C), RS1002743396 (3:50278161 C>T), RS1002747349 (3:50288424 A>T), RS1003012457 (3:50277890 C>T), RS1005620965 (3:50283229 C>A,T), RS1005784357 (3:50276006 G>A), RS1006172581 (3:50283495 C>G,T), RS1006631896 (3:50284804 G>A)

Disease associations

OMIM: gene MIM:621358 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

10 associations (top):

Study	Trait	p-value
GCST005951_49	Body mass index	1.000000e-08
GCST007559_24	Sleep duration (short sleep)	3.000000e-08
GCST008843_1	Depressive symptom (appetite changes) (binary trait)	9.000000e-09
GCST008848_2	Depressive symptoms (sum-score)	1.000000e-09
GCST008849_3	Depressive symptoms (binary sum-score)	1.000000e-10
GCST010698_80	Subcortical volume (min-P)	3.000000e-24
GCST010699_110	Brain morphology (min-P)	4.000000e-08
GCST010701_52	Cortical surface area (MOSTest)	1.000000e-16
GCST010702_36	Subcortical volume (MOSTest)	1.000000e-10
GCST010703_262	Brain morphology (MOSTest)	2.000000e-13

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0007006	depressive symptom measurement
EFO:0004346	neuroimaging measurement

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
sodium arsenite	decreases expression, increases expression	2
aristolochic acid I	increases expression	1
ethyl-p-hydroxybenzoate	decreases expression	1
beta-lapachone	increases expression	1
Sunitinib	decreases expression	1
Doxorubicin	increases expression	1
Estradiol	increases expression	1
Tobacco Smoke Pollution	increases expression	1
Valproic Acid	increases methylation	1

Clinical trials (associated diseases)

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