LSMEM1

Summary

LSMEM1 (leucine rich single-pass membrane protein 1, HGNC:22036) is a protein-coding gene on chromosome 7q31.1, encoding Leucine-rich single-pass membrane protein 1 (Q8N8F7).

Predicted to be located in membrane.

Source: NCBI Gene 286006 — RefSeq curated summary.

At a glance

• GWAS associations: 6
• Clinical variants (ClinVar): 19 total — 1 likely-pathogenic
• MANE Select transcript: NM_182597

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:22036
Approved symbol	LSMEM1
Name	leucine rich single-pass membrane protein 1
Location	7q31.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ39575
Ensembl gene	ENSG00000181016
Ensembl biotype	protein_coding
Entrez	286006

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 5 protein_coding, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000312849, ENST00000439068, ENST00000455302, ENST00000471030, ENST00000486022, ENST00000892714, ENST00000892715, ENST00000892716

RefSeq mRNA: 2 — MANE Select: NM_182597 NM_001134468, NM_182597

CCDS: CCDS5756

Canonical transcript exons

ENST00000312849 — 4 exons

Exon	Start	End
ENSE00001250537	112480991	112481346
ENSE00001250544	112489810	112491062
ENSE00001250553	112484812	112484943
ENSE00003675000	112486923	112487051

Expression profiles

Bgee: expression breadth ubiquitous, 136 present calls, max score 90.36.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0437 / max 17.6630, expressed in 12 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
80540	0.0437	12

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
hindlimb stylopod muscle	UBERON:0004252	90.36	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.12	gold quality
blood	UBERON:0000178	85.12	gold quality
body of pancreas	UBERON:0001150	84.58	gold quality
muscle of leg	UBERON:0001383	84.32	gold quality
gastrocnemius	UBERON:0001388	82.93	gold quality
lower esophagus mucosa	UBERON:0035834	82.63	gold quality
skeletal muscle tissue	UBERON:0001134	82.61	gold quality
right lobe of liver	UBERON:0001114	81.50	gold quality
cerebellar hemisphere	UBERON:0002245	79.64	gold quality
cerebellar cortex	UBERON:0002129	79.61	gold quality
cerebellum	UBERON:0002037	79.16	gold quality
right hemisphere of cerebellum	UBERON:0014890	78.11	gold quality
mucosa of stomach	UBERON:0001199	77.72	gold quality
right lung	UBERON:0002167	77.47	gold quality
mucosa of transverse colon	UBERON:0004991	77.43	gold quality
popliteal artery	UBERON:0002250	76.15	gold quality
tibial artery	UBERON:0007610	76.13	gold quality
muscle tissue	UBERON:0002385	75.27	gold quality
ascending aorta	UBERON:0001496	74.94	gold quality
right coronary artery	UBERON:0001625	74.87	gold quality
thoracic aorta	UBERON:0001515	74.75	gold quality
endometrium	UBERON:0001295	74.70	gold quality
pancreas	UBERON:0001264	74.44	gold quality
body of stomach	UBERON:0001161	74.19	gold quality
spleen	UBERON:0002106	74.16	gold quality
fundus of stomach	UBERON:0001160	74.01	gold quality
metanephros cortex	UBERON:0010533	73.35	gold quality
right adrenal gland cortex	UBERON:0035827	72.90	gold quality
omental fat pad	UBERON:0010414	72.86	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.07

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

48 targeting LSMEM1, 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-3162-3P	100.00	65.37	363
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-454-3P	99.91	74.01	1925
HSA-MIR-130B-3P	99.90	73.27	1850
HSA-MIR-130A-3P	99.90	73.31	1861
HSA-MIR-301A-3P	99.90	73.15	1839
HSA-MIR-301B-3P	99.90	73.19	1836
HSA-MIR-3666	99.90	73.24	1833
HSA-MIR-4295	99.90	73.11	1838
HSA-MIR-3686	99.90	70.53	2432
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-6875-3P	99.82	70.26	2983
HSA-MIR-204-5P	99.79	71.62	2439
HSA-MIR-211-5P	99.79	71.65	2440
HSA-MIR-4755-5P	99.71	70.34	2716
HSA-MIR-5006-3P	99.71	70.26	2728
HSA-MIR-4762-5P	99.57	68.54	1424
HSA-MIR-4761-5P	99.51	66.69	804
HSA-MIR-183-3P	99.41	69.41	1598
HSA-MIR-18A-5P	99.29	71.05	806
HSA-MIR-18B-5P	99.29	71.05	806
HSA-MIR-544B	99.18	67.41	1632
HSA-MIR-4292	99.16	65.57	1767
HSA-MIR-6791-5P	99.16	65.92	1844
HSA-MIR-4735-3P	99.14	69.85	777
HSA-MIR-4711-3P	98.97	66.87	1020
HSA-MIR-6840-3P	98.68	65.95	1923
HSA-MIR-1237-3P	98.55	67.65	1423
HSA-MIR-550A-3P	98.37	69.61	632
HSA-MIR-4717-5P	98.19	67.97	894

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Lsmem1	ENSMUSG00000071342
rattus_norvegicus	Lsmem1	ENSRNOG00000039110

Protein

Protein identifiers

Leucine-rich single-pass membrane protein 1 — Q8N8F7 (reviewed: Q8N8F7)

All UniProt accessions (1): Q8N8F7

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8N8F7-1	1	yes
Q8N8F7-2	2

RefSeq proteins (2): NP_001127940, NP_872403* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR028099	DUF4577	Family

Pfam: PF15145

UniProt features (5 total): chain 1, transmembrane region 1, coiled-coil region 1, modified residue 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N8F7-F1	68.68	0.23

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 24

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 27 (showing top): CHANDRAN_METASTASIS_UP, chr7q31, ZNF10_TARGET_GENES, MIR454_3P, MIR130A_3P, MIR130B_3P, MIR4295, MIR301A_3P, MIR301B_3P, MIR3666, MIR1237_3P, MIR4711_3P, MIR3139, MIR708_5P, MIR28_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

416 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LSMEM1	ETNPPL	Q8TBG4	490
LSMEM1	ZBTB1	Q9Y2K1	489
LSMEM1	ITPRIP	Q8IWB1	488
LSMEM1	REPS2	Q8NFH8	461
LSMEM1	WDR47	O94967	459
LSMEM1	ZFAND2A	Q8N6M9	447
LSMEM1	TMCC3	Q9ULS5	431
LSMEM1	C3orf62	Q6ZUJ4	419
LSMEM1	UBALD2	Q8IYN6	400
LSMEM1	PLPPR2	Q96GM1	370
LSMEM1	PPP1R3A	Q16821	350
LSMEM1	C6orf58	Q6P5S2	350
LSMEM1	CABCOCO1	Q8IVU9	348
LSMEM1	MANSC1	Q9H8J5	348
LSMEM1	CELSR1	Q9NYQ6	341

IntAct

22 interactions, top by confidence:

A	B	Type	Score
LSMEM1	LSMEM2	psi-mi:“MI:0915”(physical association)	0.720
LSMEM2	LSMEM1	psi-mi:“MI:0915”(physical association)	0.720
MAL	LSMEM1	psi-mi:“MI:0915”(physical association)	0.560
LSMEM1	ZDHHC15	psi-mi:“MI:0915”(physical association)	0.560
CD53	LSMEM1	psi-mi:“MI:0915”(physical association)	0.560
LSMEM1	TMEM80	psi-mi:“MI:0915”(physical association)	0.560
LSMEM1	SRC	psi-mi:“MI:0914”(association)	0.350
LSMEM2	LSMEM1	psi-mi:“MI:0915”(physical association)	0.000
ZDHHC15	LSMEM1	psi-mi:“MI:0915”(physical association)	0.000
LSMEM1	TMEM80	psi-mi:“MI:0915”(physical association)	0.000
LSMEM1	CD53	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (13): LSMEM1 (Two-hybrid), LSMEM1 (Two-hybrid), LSMEM1 (Two-hybrid), LSMEM1 (Two-hybrid), LSMEM1 (Two-hybrid), LSMEM1 (Two-hybrid), SRC (Affinity Capture-MS), IFNGR2 (Affinity Capture-MS), PPP1R10 (Affinity Capture-MS), FBXO28 (Affinity Capture-MS), LSMEM1 (PCA), LSMEM1 (PCA), APP (Reconstituted Complex)

ESM2 similar proteins: A2VE00, A5PK14, F1QEA1, O75324, P0DKX4, P20826, P21581, P21583, P58550, P59773, P61807, P61808, P79169, P79368, Q06220, Q09108, Q10589, Q15053, Q17Q87, Q28132, Q28C41, Q28GJ0, Q29030, Q2T9X8, Q3UQS2, Q5PQQ9, Q5RBY6, Q5RKG1, Q5U3Z6, Q640L3, Q6AY06, Q6DF94, Q6IQY5, Q6NRX3, Q811A2, Q86YF9, Q8BIS8, Q8BMD2, Q8C804, Q8N0Z3

Diamond homologs: A5PK14, Q3UQS2, Q8N8F7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	14
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
815018	GRCh37/hg19 7q31.1(chr7:109594999-113885203)x3	Likely pathogenic

SpliceAI

619 predictions. Top by Δscore:

Variant	Effect	Δscore
7:112489805:T:TA	acceptor_gain	1.0000
7:112489808:A:AG	acceptor_gain	1.0000
7:112489809:G:GG	acceptor_gain	1.0000
7:112480974:A:G	donor_gain	0.9900
7:112484939:GTTCC:G	donor_gain	0.9900
7:112484944:G:GG	donor_gain	0.9900
7:112484958:G:T	donor_gain	0.9900
7:112486917:T:G	acceptor_gain	0.9900
7:112486921:A:AG	acceptor_gain	0.9900
7:112486922:G:GG	acceptor_gain	0.9900
7:112487052:G:GG	donor_gain	0.9900
7:112487052:GTAA:G	donor_loss	0.9900
7:112489806:GAA:G	acceptor_loss	0.9900
7:112489808:AG:A	acceptor_loss	0.9900
7:112489809:GTT:G	acceptor_gain	0.9900
7:112489809:GTTC:G	acceptor_gain	0.9900
7:112484859:G:GT	donor_gain	0.9800
7:112484958:G:GT	donor_gain	0.9800
7:112486916:A:AG	acceptor_gain	0.9800
7:112487053:T:A	donor_loss	0.9800
7:112487054:AA:A	donor_loss	0.9800
7:112489809:GTTCA:G	acceptor_gain	0.9800
7:112480979:G:GT	donor_gain	0.9700
7:112486910:T:A	acceptor_loss	0.9700
7:112486910:T:TA	acceptor_gain	0.9700
7:112486919:TTAG:T	acceptor_loss	0.9700
7:112486920:TAGC:T	acceptor_loss	0.9700
7:112486921:AG:A	acceptor_loss	0.9700
7:112486922:G:GA	acceptor_loss	0.9700
7:112486922:GCTCT:G	acceptor_gain	0.9700

AlphaMissense

855 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:112487015:A:C	S74R	0.992
7:112487017:C:A	S74R	0.992
7:112487017:C:G	S74R	0.992
7:112489879:T:C	L109P	0.978
7:112484899:T:C	L28S	0.961
7:112489879:T:A	L109H	0.960
7:112489849:T:C	L99P	0.942
7:112484890:T:C	I25T	0.937
7:112484886:T:C	S24P	0.927
7:112484884:A:T	D23V	0.923
7:112484887:C:T	S24F	0.922
7:112489891:A:T	N113I	0.922
7:112484890:T:A	I25K	0.902
7:112484894:T:A	N26K	0.901
7:112484894:T:G	N26K	0.901
7:112489912:T:C	L120P	0.890
7:112489879:T:G	L109R	0.887
7:112484893:A:T	N26I	0.881
7:112487019:T:C	L75P	0.881
7:112484885:T:A	D23E	0.880
7:112484885:T:G	D23E	0.880
7:112484887:C:A	S24Y	0.878
7:112484890:T:G	I25R	0.870
7:112484883:G:C	D23H	0.863
7:112484884:A:C	D23A	0.858
7:112489883:G:C	K110N	0.857
7:112489883:G:T	K110N	0.857
7:112487007:T:G	L71R	0.851
7:112489900:T:G	I116S	0.848
7:112489892:T:A	N113K	0.846

dbSNP variants (sampled 300 via entrez): RS1000006355 (7:112483900 A>G), RS1000505556 (7:112481076 A>G), RS1000736857 (7:112490608 C>G), RS1000888135 (7:112481458 A>T), RS1001061077 (7:112485604 T>A,C), RS1001894462 (7:112478960 T>C), RS1002059271 (7:112486267 G>T), RS1002226373 (7:112487200 C>T), RS1002286475 (7:112480592 G>A), RS1002959992 (7:112487082 A>T), RS1002993872 (7:112481004 C>T), RS1003114369 (7:112485607 C>T), RS1003882397 (7:112487873 C>T), RS1004413012 (7:112482293 C>G), RS1005343559 (7:112479446 C>G,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

6 associations (top):

Study	Trait	p-value
GCST010796_570	Electrocardiogram morphology (amplitude at temporal datapoints)	4.000000e-09
GCST010796_571	Electrocardiogram morphology (amplitude at temporal datapoints)	6.000000e-09
GCST010796_572	Electrocardiogram morphology (amplitude at temporal datapoints)	3.000000e-08
GCST010796_573	Electrocardiogram morphology (amplitude at temporal datapoints)	4.000000e-09
GCST010796_574	Electrocardiogram morphology (amplitude at temporal datapoints)	2.000000e-09
GCST010796_575	Electrocardiogram morphology (amplitude at temporal datapoints)	1.000000e-09

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004327	electrocardiography

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

47 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
(+)-JQ1 compound	increases expression	2
Benzo(a)pyrene	affects methylation, increases methylation	2
Silicon Dioxide	increases expression	2
Tobacco Smoke Pollution	increases expression	2
Valproic Acid	affects expression, decreases methylation	2
aristolochic acid I	increases expression	1
methylmercuric chloride	increases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	increases methylation	1
sodium arsenate	increases abundance, increases expression	1
2-methyl-4-isothiazolin-3-one	increases expression	1
trichostatin A	affects expression	1
hydroxyhydroquinone	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
sodium arsenite	increases expression	1
butyraldehyde	increases expression	1
benzo(e)pyrene	decreases methylation	1
potassium chromate(VI)	affects cotreatment, increases expression	1
ferrous chloride	increases expression	1
aflatoxin B2	decreases methylation	1
S-(1,2-dichlorovinyl)cysteine	affects cotreatment, increases expression	1
epigallocatechin gallate	affects cotreatment, increases expression	1
abrine	increases expression	1
(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)	decreases expression	1
licochalcone B	increases expression	1
jinfukang	affects cotreatment, decreases expression	1
theaflavin-3,3’-digallate	affects expression	1
Acetaminophen	increases expression	1
Arsenic	increases abundance, increases expression	1
Cisplatin	decreases expression, affects cotreatment	1

Clinical trials (associated diseases)

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