LRTM3

Summary

LRTM3 (leucine rich repeat transmembrane protein 3, HGNC:26851) is a protein-coding gene on chromosome 13q33.1, encoding Leucine-rich repeat transmembrane protein 3 (Q8NDH2).

Predicted to be located in membrane.

Source: NCBI Gene 643677 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 677 total
• MANE Select transcript: NM_001146197

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26851
Approved symbol	LRTM3
Name	leucine rich repeat transmembrane protein 3
Location	13q33.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ40176
Ensembl gene	ENSG00000175820
Ensembl biotype	protein_coding
Entrez	643677

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000322527

RefSeq mRNA: 1 — MANE Select: NM_001146197 NM_001146197

CCDS: CCDS73596

Canonical transcript exons

ENST00000322527 — 4 exons

Exon	Start	End
ENSE00001224565	102729367	102750388
ENSE00003713915	102758410	102758452
ENSE00003724621	102758543	102758576
ENSE00003737691	102758702	102759072

Expression profiles

Bgee: expression breadth broad, 15 present calls, max score 98.48.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0254 / max 23.4564, expressed in 4 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
138107	0.0254	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	98.48	gold quality
buccal mucosa cell	CL:0002336	85.89	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.35	gold quality
left testis	UBERON:0004533	71.98	gold quality
right testis	UBERON:0004534	71.20	gold quality
testis	UBERON:0000473	70.44	gold quality
colonic epithelium	UBERON:0000397	52.43	gold quality
ventricular zone	UBERON:0003053	49.74	gold quality
bone marrow cell	CL:0002092	49.45	gold quality
adult organism	UBERON:0007023	48.98	silver quality
ganglionic eminence	UBERON:0004023	48.53	gold quality
hindlimb stylopod muscle	UBERON:0004252	48.53	silver quality
skin of hip	UBERON:0001554	46.13	silver quality
sural nerve	UBERON:0015488	46.00	gold quality
lower lobe of lung	UBERON:0008949	45.07	silver quality
middle temporal gyrus	UBERON:0002771	44.65	gold quality
apex of heart	UBERON:0002098	44.48	silver quality
bone marrow	UBERON:0002371	43.38	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
cortical plate	UBERON:0005343	43.30	gold quality
liver	UBERON:0002107	43.22	gold quality
skeletal muscle tissue	UBERON:0001134	43.07	gold quality
muscle tissue	UBERON:0002385	42.80	gold quality
cauda epididymis	UBERON:0004360	42.79	gold quality
secondary oocyte	CL:0000655	42.57	gold quality
right atrium auricular region	UBERON:0006631	41.63	silver quality
cardiac atrium	UBERON:0002081	41.58	silver quality
islet of Langerhans	UBERON:0000006	41.44	gold quality
vastus lateralis	UBERON:0001379	41.41	gold quality
quadriceps femoris	UBERON:0001377	41.37	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.13

Regulation

Is transcription factor: no

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ccdc168	ENSMUSG00000091844

Protein

Protein identifiers

Leucine-rich repeat transmembrane protein 3 — Q8NDH2 (reviewed: Q8NDH2)

Alternative names: Coiled-coil domain-containing protein 168

All UniProt accessions (1): Q8NDH2

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (1): NP_001139669* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031624	CCDC168_N	Domain
IPR053366	LRR_transmembrane	Family

Pfam: PF15804

UniProt features (86 total): compositionally biased region 23, region of interest 22, repeat 20, sequence variant 15, sequence conflict 4, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

No AlphaFold model available for Q8NDH2 — AlphaFold DB does not currently provide models for proteins above ~3000 aa.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 12 (showing top): ID2_TARGET_GENES, ZNF664_TARGET_GENES, chr13q33, GSE17974_IL4_AND_ANTI_IL12_VS_UNTREATED_24H_ACT_CD4_TCELL_DN, GSE18791_UNSTIM_VS_NEWCATSLE_VIRUS_DC_10H_UP, GSE2770_IL12_ACT_VS_ACT_CD4_TCELL_6H_DN, GSE25088_CTRL_VS_IL4_STIM_STAT6_KO_MACROPHAGE_UP, GSE25123_WT_VS_PPARG_KO_MACROPHAGE_ROSIGLITAZONE_STIM_DN, GSE16385_UNTREATED_VS_12H_ROSIGLITAZONE_TREATED_MACROPHAGE_UP, FLORIO_NEOCORTEX_BASAL_RADIAL_GLIA_UP, FLORIO_HUMAN_NEOCORTEX, GSE34156_UNTREATED_VS_24H_NOD2_AND_TLR1_TLR2_LIGAND_TREATED_MONOCYTE_UP

GO Biological Process (0):

GO Molecular Function (0):

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	1

Protein interactions and networks

STRING

300 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LRTM3	ZNF563	Q8TA94	503
LRTM3	RNF223	E7ERA6	489
LRTM3	FBF1	Q8TES7	459
LRTM3	VPS33A	Q96AX1	458
LRTM3	SLC17A9	Q9BYT1	457
LRTM3	A0A2R8YFG2	A0A2R8YFG2	453
LRTM3	MEAF6	Q9HAF1	452
LRTM3	FSIP2	Q5CZC0	435
LRTM3	ASTE1	Q2TB18	431
LRTM3	RBM5	P52756	425
LRTM3	CLCN3	P51790	416
LRTM3	ADGRV1	Q8WXG9	415
LRTM3	EXOSC10	Q01780	410
LRTM3	PTK6	Q13882	408
LRTM3	RUVBL2	Q9Y230	405

IntAct

8 interactions, top by confidence:

A	B	Type	Score
CCDC168	H1-5	psi-mi:“MI:0915”(physical association)	0.400
CCDC168	HSPA5	psi-mi:“MI:0915”(physical association)	0.400
	ESYT2	psi-mi:“MI:0914”(association)	0.350
M		psi-mi:“MI:0914”(association)	0.350
BMI1	MEIS3P1	psi-mi:“MI:0914”(association)	0.350
CYBB	CYBA	psi-mi:“MI:0914”(association)	0.350
MST1R	SHTN1	psi-mi:“MI:2364”(proximity)	0.270

ESM2 similar proteins: A0A1B0GTH6, A0A1D5RMD1, A1KXM5, A2AEY4, A6NCI8, A6QQS3, A7KBS4, C4P6S0, O94713, P0C9Z7, P53963, P53976, Q0P670, Q0VAV2, Q10668, Q196W1, Q2KHR3, Q2YDJ5, Q32MG2, Q3V0A6, Q3V3Q4, Q4V8E9, Q5JRM2, Q68FV4, Q6AXV6, Q6AYN3, Q6NS59, Q7TSG5, Q80VJ6, Q80Y39, Q80YD3, Q810T2, Q86XD8, Q8C5U4, Q8CH19, Q8IWI9, Q8K4E0, Q8NDH2, Q8NEV8, Q8NFU7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	568
Likely benign	95
Benign	12

Top pathogenic / likely-pathogenic (0)

SpliceAI

311 predictions. Top by Δscore:

Variant	Effect	Δscore
13:102758539:TTA:T	donor_loss	1.0000
13:102758540:TAC:T	donor_loss	1.0000
13:102758541:A:AC	donor_gain	1.0000
13:102758542:C:CG	donor_gain	1.0000
13:102750384:CAACT:C	acceptor_gain	0.9900
13:102750387:CT:C	acceptor_gain	0.9900
13:102750389:C:CC	acceptor_gain	0.9900
13:102758541:AC:A	donor_gain	0.9900
13:102758542:CC:C	donor_gain	0.9900
13:102758542:CCA:C	donor_gain	0.9900
13:102758542:CCAA:C	donor_gain	0.9900
13:102758542:CCAAG:C	donor_gain	0.9900
13:102750386:ACTC:A	acceptor_loss	0.9800
13:102750388:TCTGA:T	acceptor_loss	0.9800
13:102750389:C:A	acceptor_loss	0.9800
13:102750390:T:A	acceptor_loss	0.9800
13:102750385:AACT:A	acceptor_gain	0.9700
13:102750386:ACT:A	acceptor_gain	0.9700
13:102750387:CTC:C	acceptor_gain	0.9700
13:102750388:TCT:T	acceptor_gain	0.9700
13:102758577:C:CC	acceptor_gain	0.9700
13:102750276:TAG:T	donor_gain	0.9600
13:102758700:ACCT:A	donor_gain	0.9600
13:102758701:CCTC:C	donor_gain	0.9600
13:102750389:C:G	acceptor_gain	0.9500
13:102758453:C:CC	acceptor_gain	0.9500
13:102758577:C:CA	acceptor_loss	0.9500
13:102758539:TTACC:T	acceptor_loss	0.9400
13:102758696:TCTTA:T	donor_loss	0.9400
13:102758697:CTTA:C	donor_loss	0.9400

AlphaMissense

46999 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000141080 (13:102754196 C>G,T), RS1000390675 (13:102748125 G>A,T), RS1000420057 (13:102731500 C>A,T), RS1000745031 (13:102742695 C>A,G), RS1000999156 (13:102749802 A>G), RS1001023680 (13:102730153 T>A), RS1001031421 (13:102736807 C>T), RS1001107864 (13:102743449 A>C,G), RS1001303159 (13:102755703 A>G,T), RS1001326788 (13:102730559 T>A,G), RS1001492843 (13:102748500 C>T), RS1001504279 (13:102748268 T>C), RS1001508719 (13:102735213 A>G), RS1001571010 (13:102756112 C>T), RS1001712782 (13:102741703 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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

6 total (human), top 6 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
versicolorin A	increases expression	1
coumarin	decreases phosphorylation	1
tebuconazole	decreases expression	1
Benzo(a)pyrene	increases mutagenesis	1
Okadaic Acid	increases expression	1

Clinical trials (associated diseases)

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