LRTM1

Summary

LRTM1 (leucine rich repeat transmembrane protein 1, HGNC:25023) is a protein-coding gene on chromosome 3p14.3, encoding Leucine-rich repeat and transmembrane domain-containing protein 1 (Q9HBL6).

Predicted to act upstream of or within positive regulation of synapse assembly. Predicted to be located in membrane.

Source: NCBI Gene 57408 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 1 total
• MANE Select transcript: NM_020678

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25023
Approved symbol	LRTM1
Name	leucine rich repeat transmembrane protein 1
Location	3p14.3
Locus type	gene with protein product
Status	Approved
Aliases	HT017
Ensembl gene	ENSG00000144771
Ensembl biotype	protein_coding
Entrez	57408

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000273286, ENST00000493075

RefSeq mRNA: 2 — MANE Select: NM_020678 NM_001304389, NM_020678

CCDS: CCDS2876, CCDS77753

Canonical transcript exons

ENST00000273286 — 3 exons

Exon	Start	End
ENSE00001377954	54927905	54928059
ENSE00001865191	54918231	54918892
ENSE00003654869	54924619	54925215

Expression profiles

Bgee: expression breadth broad, 51 present calls, max score 97.73.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 3.2009 / max 2796.4272, expressed in 52 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter ID	TPM avg	Samples expressed
42537	2.2208	32
42536	0.5692	25
42539	0.1301	18
42535	0.1145	16
42538	0.0454	6
42540	0.0425	6
202778	0.0331	7
202777	0.0287	5
42541	0.0167	7

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
pineal body	UBERON:0001905	97.73	gold quality
buccal mucosa cell	CL:0002336	86.57	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.05	gold quality
pancreatic ductal cell	CL:0002079	75.09	silver quality
spleen	UBERON:0002106	73.00	gold quality
tibialis anterior	UBERON:0001385	68.01	silver quality
pharyngeal mucosa	UBERON:0000355	64.32	gold quality
Brodmann (1909) area 23	UBERON:0013554	62.24	silver quality
ileal mucosa	UBERON:0000331	60.22	silver quality
tendon of biceps brachii	UBERON:0008188	60.22	gold quality
vena cava	UBERON:0004087	58.69	gold quality
deltoid	UBERON:0001476	56.73	gold quality
tendon	UBERON:0000043	56.12	silver quality
middle temporal gyrus	UBERON:0002771	55.44	gold quality
choroid plexus epithelium	UBERON:0003911	55.17	gold quality
calcaneal tendon	UBERON:0003701	54.61	gold quality
medial globus pallidus	UBERON:0002477	54.01	gold quality
primary visual cortex	UBERON:0002436	53.99	silver quality
epithelial cell of pancreas	CL:0000083	53.81	gold quality
quadriceps femoris	UBERON:0001377	53.74	gold quality
cerebellar vermis	UBERON:0004720	52.31	gold quality
vastus lateralis	UBERON:0001379	52.16	gold quality
occipital lobe	UBERON:0002021	51.04	silver quality
globus pallidus	UBERON:0001875	51.01	gold quality
lower lobe of lung	UBERON:0008949	50.60	silver quality
Brodmann (1909) area 46	UBERON:0006483	49.60	gold quality
oviduct epithelium	UBERON:0004804	49.43	gold quality
blood vessel layer	UBERON:0004797	49.29	gold quality
cervix squamous epithelium	UBERON:0006922	49.20	gold quality
hair follicle	UBERON:0002073	49.18	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-MTAB-7316	yes	865.74
E-GEOD-137537	yes	22.05
E-ANND-3	no	2.42

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

5 targeting LRTM1, 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-548P	99.98	72.25	3784
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-182-5P	99.87	74.03	2589
HSA-MIR-3922-3P	99.25	64.96	1136
HSA-MIR-511-5P	98.97	70.94	2268

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	lrtm1	ENSDARG00000098742
mus_musculus	Lrtm1	ENSMUSG00000045776
rattus_norvegicus		ENSRNOG00000067759

Paralogs (22): DCN (ENSG00000011465), RTN4R (ENSG00000040608), ASPN (ENSG00000106819), FLRT3 (ENSG00000125848), FLRT1 (ENSG00000126500), LRRC4 (ENSG00000128594), LRRC4B (ENSG00000131409), PODNL1 (ENSG00000132000), LRRC4C (ENSG00000148948), LRRTM1 (ENSG00000162951), LRRC15 (ENSG00000172061), PODN (ENSG00000174348), LRRTM4 (ENSG00000176204), BGN (ENSG00000182492), LRRC19 (ENSG00000184434), FLRT2 (ENSG00000185070), GP1BA (ENSG00000185245), RTN4RL1 (ENSG00000185924), RTN4RL2 (ENSG00000186907), NYX (ENSG00000188937), LRRC66 (ENSG00000188993), LRRTM3 (ENSG00000198739)

Protein

Protein identifiers

Leucine-rich repeat and transmembrane domain-containing protein 1 — Q9HBL6 (reviewed: Q9HBL6)

All UniProt accessions (1): Q9HBL6

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9HBL6-1	1	yes
Q9HBL6-2	2

RefSeq proteins (2): NP_001291318, NP_065729* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000483	Cys-rich_flank_reg_C	Domain
IPR001611	Leu-rich_rpt	Repeat
IPR003591	Leu-rich_rpt_typical-subtyp	Repeat
IPR032675	LRR_dom_sf	Homologous_superfamily
IPR050541	LRR_TM_domain-containing	Family

Pfam: PF13855

UniProt features (19 total): repeat 5, domain 2, glycosylation site 2, sequence variant 2, topological domain 2, signal peptide 1, chain 1, region of interest 1, compositionally biased region 1, splice variant 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9HBL6-F1	81.71	0.67

Functional residue map

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

Glycosylation sites (2): 104, 147

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 39 (showing top): CAGCTG_AP4_Q5, EVI1_05, FREAC3_01, WTGAAAT_UNKNOWN, MODULE_207, P53_DECAMER_Q2, chr3p14, OSF2_Q6, RP58_01, E47_02, ATF2_UP.V1_UP, BRCA1_DN.V1_UP, CTIP_DN.V1_UP, ZNF7_TARGET_GENES, MIR10527_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

678 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LRTM1	CORIN	Q9Y5Q5	431
LRTM1	ERC2	O15083	383
LRTM1	CACNA2D3	Q8IZS8	382
LRTM1	CACNG6	Q9BXT2	353
LRTM1	CCL3L1	P16619	353
LRTM1	STAT6	P42226	349
LRTM1	ACTR8	Q9H981	345
LRTM1	ADPRHL1	Q8NDY3	333
LRTM1	HEPHL1	Q6MZM0	328
LRTM1	KIAA0586	Q9BVV6	322
LRTM1	C21orf58	P58505	320
LRTM1	TMEM215	Q68D42	314
LRTM1	TRPM1	Q7Z4N2	309
LRTM1	FAM81B	Q96LP2	308
LRTM1	OPN1SW	P03999	306

IntAct

5 interactions, top by confidence:

A	B	Type	Score
MAL	LRTM1	psi-mi:“MI:0915”(physical association)	0.560
LRTM1	PTPRF	psi-mi:“MI:0914”(association)	0.350
MAL	LRTM1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (7): PITHD1 (Affinity Capture-MS), MAL (Two-hybrid), PTPRF (Affinity Capture-MS), GNPDA2 (Affinity Capture-MS), UBA3 (Affinity Capture-MS), ATPAF2 (Affinity Capture-MS), NAE1 (Affinity Capture-MS)

ESM2 similar proteins: A3KNN3, A4IFA6, A6H789, A6H793, A6NDA9, A8WHP9, E7FE13, O08644, O08742, O08770, O14498, O15197, P0C0K6, P0C0K7, P14616, P14617, P21709, P54760, P54761, P59034, P59035, Q149C3, Q3ZBI5, Q5BK65, Q5JZY3, Q5NVQ6, Q5R7M3, Q60750, Q62178, Q64716, Q6GU68, Q6P7C4, Q6PFC5, Q6UY18, Q80ZD5, Q86SJ2, Q86WK7, Q86YC3, Q8BGX3, Q8BMT4

Diamond homologs: A3KNN3, A6H789, A6H793, A6NJW4, A8WHP9, E7FE13, F1MLX5, G5EFX6, O02678, O02833, O35367, O46378, O46379, O46542, O60938, O62702, O75093, O75094, O88279, O88280, O94813, P07359, P07585, P21793, P24014, P28654, P28675, P35858, P35859, P51884, P51885, P51886, P51888, P51890, P58874, P59034, P59035, P70186, P70389, P83286

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

481 predictions. Top by Δscore:

Variant	Effect	Δscore
3:54918891:CCCTT:C	acceptor_gain	1.0000
3:54918892:CCTT:C	acceptor_gain	1.0000
3:54918895:T:TC	acceptor_gain	1.0000
3:54918889:CCCC:C	acceptor_gain	0.9900
3:54918890:CCC:C	acceptor_gain	0.9900
3:54918890:CCCC:C	acceptor_gain	0.9900
3:54918891:CC:C	acceptor_gain	0.9900
3:54918891:CCCT:C	acceptor_loss	0.9900
3:54918892:CC:C	acceptor_loss	0.9900
3:54918893:C:CC	acceptor_gain	0.9900
3:54918893:C:CG	acceptor_loss	0.9900
3:54918894:T:A	acceptor_loss	0.9900
3:54918894:T:C	acceptor_gain	0.9900
3:54918895:T:C	acceptor_gain	0.9900
3:54918888:TCCCC:T	acceptor_gain	0.9800
3:54918889:CCCCC:C	acceptor_gain	0.9800
3:54918893:C:T	acceptor_gain	0.9800
3:54927899:GCTCA:G	donor_loss	0.9800
3:54927900:CTCA:C	donor_loss	0.9800
3:54927901:TCACC:T	donor_loss	0.9800
3:54927902:CACC:C	donor_loss	0.9800
3:54927903:A:C	donor_loss	0.9800
3:54927904:CCTT:C	donor_loss	0.9800
3:54925141:G:T	donor_gain	0.9600
3:54918894:T:TC	acceptor_gain	0.9500
3:54918903:C:CT	acceptor_gain	0.9500
3:54927898:GGCTC:G	donor_loss	0.9300
3:54918904:A:T	acceptor_gain	0.9200
3:54918892:CCTTT:C	acceptor_gain	0.9000
3:54918893:CTTT:C	acceptor_gain	0.8900

AlphaMissense

2234 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:54924677:C:A	W182C	0.992
3:54924677:C:G	W182C	0.992
3:54924679:A:G	W182R	0.988
3:54924679:A:T	W182R	0.988
3:54924909:A:G	L105P	0.985
3:54918868:C:G	C210S	0.983
3:54918869:A:T	C210S	0.983
3:54924672:C:G	C184S	0.983
3:54924673:A:T	C184S	0.983
3:54924915:A:G	L103S	0.983
3:54925038:A:G	I62T	0.982
3:54924987:A:G	L79S	0.981
3:54925053:A:G	L57S	0.981
3:54925116:C:G	C36S	0.979
3:54925117:A:T	C36S	0.979
3:54925014:A:C	F70C	0.978
3:54918868:C:T	C210Y	0.977
3:54924971:A:C	N84K	0.977
3:54924971:A:T	N84K	0.977
3:54925059:A:G	L55P	0.974
3:54924828:T:A	N132I	0.973
3:54924899:A:C	N108K	0.973
3:54924899:A:T	N108K	0.973
3:54924981:A:G	L81S	0.971
3:54925115:G:C	C36W	0.971
3:54924924:A:C	L100W	0.970
3:54924843:A:G	L127P	0.969
3:54925044:T:A	N60I	0.968
3:54918869:A:G	C210R	0.967
3:54924678:C:G	W182S	0.967

dbSNP variants (sampled 300 via entrez): RS1000028458 (3:54932504 A>T), RS1000066392 (3:54965680 G>A), RS1000080299 (3:54932659 T>G), RS1000183555 (3:54964551 C>A,T), RS1000187815 (3:54936929 G>A,C,T), RS1000194215 (3:54961514 A>C), RS1000235094 (3:54958227 G>A), RS1000245591 (3:54944120 T>A), RS1000323717 (3:54938528 C>T), RS1000502742 (3:54922714 A>G), RS1000519075 (3:54965589 G>C), RS1000556598 (3:54923052 A>G), RS1000582851 (3:54942946 C>G,T), RS1000623094 (3:54950132 T>C), RS1000626051 (3:54954357 A>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
GCST002304_24	Fractional exhaled nitric oxide (childhood)	3.000000e-06
GCST003542_189	Night sleep phenotypes	6.000000e-06
GCST008171_30	Platelet aggregation	5.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0005536	nitric oxide exhalation measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs6806020	CACNA2D3, LRTM1		0.00	0

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
CGP 52608	affects binding, increases reaction	1
Resveratrol	affects cotreatment, decreases expression	1
Benzo(a)pyrene	increases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Valproic Acid	affects expression	1

Clinical trials (associated diseases)

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