LRIG3

Summary

LRIG3 (leucine rich repeats and immunoglobulin like domains 3, HGNC:30991) is a protein-coding gene on chromosome 12q14.1, encoding Leucine-rich repeats and immunoglobulin-like domains protein 3 (Q6UXM1). May play a role in craniofacial and inner ear morphogenesis during embryonic development.

Predicted to act upstream of or within otolith morphogenesis. Located in extracellular space.

Source: NCBI Gene 121227 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 146 total
• Cancer driver (intOGen): loss-of-function (tumor-suppressor-like) across 1 cancer types
• MANE Select transcript: NM_153377

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30991
Approved symbol	LRIG3
Name	leucine rich repeats and immunoglobulin like domains 3
Location	12q14.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ90440, KIAA3016
Ensembl gene	ENSG00000139263
Ensembl biotype	protein_coding
OMIM	608870
Entrez	121227

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 5 protein_coding, 4 retained_intron, 1 nonsense_mediated_decay

ENST00000320743, ENST00000379141, ENST00000433272, ENST00000547329, ENST00000548968, ENST00000550304, ENST00000550825, ENST00000552267, ENST00000552646, ENST00000900032

RefSeq mRNA: 2 — MANE Select: NM_153377 NM_001136051, NM_153377

CCDS: CCDS44933, CCDS8960

Canonical transcript exons

ENST00000320743 — 19 exons

Exon	Start	End
ENSE00000937272	58882869	58883032
ENSE00000937273	58880581	58880901
ENSE00001241759	58883520	58883591
ENSE00001351957	58885831	58885902
ENSE00001366244	58889996	58890139
ENSE00001368584	58890665	58890796
ENSE00001369498	58913982	58914056
ENSE00001374953	58888329	58888472
ENSE00001376441	58888819	58888962
ENSE00001386114	58886810	58886890
ENSE00001387568	58887789	58887932
ENSE00002378601	58920000	58920504
ENSE00003481884	58878824	58879105
ENSE00003491169	58876445	58876603
ENSE00003665127	58874055	58874330
ENSE00003671102	58874430	58874573
ENSE00003671348	58877400	58877852
ENSE00003673121	58914265	58914336
ENSE00003903197	58872155	58872816

Expression profiles

Bgee: expression breadth ubiquitous, 218 present calls, max score 97.13.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.1997 / max 387.1491, expressed in 1431 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
131793	5.3896	1202
131789	1.8899	1044
131794	0.9931	551
131790	0.8673	569
131791	0.7115	445
131795	0.6779	414
131788	0.5587	311
131792	0.1118	25

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	97.13	gold quality
right lobe of thyroid gland	UBERON:0001119	94.42	gold quality
skin of leg	UBERON:0001511	94.32	gold quality
skin of abdomen	UBERON:0001416	94.23	gold quality
left lobe of thyroid gland	UBERON:0001120	94.17	gold quality
minor salivary gland	UBERON:0001830	93.99	gold quality
thyroid gland	UBERON:0002046	93.97	gold quality
rectum	UBERON:0001052	93.55	gold quality
zone of skin	UBERON:0000014	93.13	gold quality
palpebral conjunctiva	UBERON:0001812	92.68	gold quality
ventricular zone	UBERON:0003053	92.44	gold quality
epithelial cell of pancreas	CL:0000083	91.91	silver quality
colonic epithelium	UBERON:0000397	91.86	gold quality
mouth mucosa	UBERON:0003729	91.76	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	91.22	gold quality
saliva-secreting gland	UBERON:0001044	91.16	gold quality
tibial nerve	UBERON:0001323	91.13	gold quality
mucosa of stomach	UBERON:0001199	91.10	gold quality
mucosa of paranasal sinus	UBERON:0005030	90.56	gold quality
body of pancreas	UBERON:0001150	89.97	gold quality
popliteal artery	UBERON:0002250	89.89	gold quality
tibial artery	UBERON:0007610	89.87	gold quality
sural nerve	UBERON:0015488	89.64	gold quality
gall bladder	UBERON:0002110	89.63	gold quality
left ovary	UBERON:0002119	89.36	gold quality
ectocervix	UBERON:0012249	89.33	gold quality
skin of hip	UBERON:0001554	89.30	gold quality
lower esophagus muscularis layer	UBERON:0035833	89.22	gold quality
lower esophagus	UBERON:0013473	89.20	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	89.11	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	11.48
E-MTAB-9388	yes	10.02
E-GEOD-109979	no	337.20

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

63 targeting LRIG3, 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-7110-3P	100.00	73.18	2486
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-196A-5P	100.00	68.16	684
HSA-MIR-196B-5P	100.00	68.16	681
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7F-5P	99.98	72.56	1784
HSA-LET-7G-5P	99.98	72.37	1784
HSA-LET-7I-5P	99.98	72.37	1788
HSA-MIR-98-5P	99.98	72.33	1787
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-433-3P	99.98	69.37	1203
HSA-LET-7D-5P	99.96	71.76	1632
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-4458	99.96	71.64	1650
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-659-3P	99.85	70.69	1620
HSA-MIR-202-3P	99.84	71.41	1290

Literature-anchored findings (GeneRIF, showing 23)

• These results indicate that expression and sub-cellular localization of LRIG1-3 might be of importance in the pathogenesis and prognosis of astrocytic tumors. (PMID:16532360)
• Down-regulation of LRIG3 in HP75 pituitary adenoma is reported. (PMID:17393120)
• LRIG proteins may have a role in epidermal homeostasis and psoriasis (PMID:18037903)
• LRIG3 may be involved in the regulation of EGF receptor signaling, and serve as a tumor suppressor gene in the pathogenesis of glioma. (PMID:19200647)
• the expression of LRIG1-3 was evaluated in 51 human ependymomas and was found to be more highly expressed in supratentorial than in infratentorial ependymomas (PMID:19216216)
• siRNA targeting LRIG3 gene shows a dramatic inhibitory effect on RNA transcription and protein expression, then promotes the proliferation and suppresses apoptosis of GL15 cells. (PMID:19224171)
• Down-regulating LRIG3 gene expression can improve the proliferation of glioma GL15 cells. (PMID:19448407)
• Silencing LRIG3 inhibited the proliferation and promoted the apoptosis of bladder cancer T24 cells. (PMID:21505989)
• High LRIG3 expression is associated with cervical adenocarcinoma progression. (PMID:23165628)
• In conclusion, the over-expression of LRIG3 could influence the cell cycle and invasion, inhibit proliferation and induce apoptosis in the three bladder cancer cell lines. (PMID:23392718)
• Data indicate that Lrig3 opposes Lrig1 negative regulatory action and enhances ErbB receptors ERBB2, ERBB3 and ERBB4 stability. (PMID:23723069)
• The results on expression of other tumor markers suggest that LRIG3 is influenced by or influences a pattern of tumor markers in cancer and precancerous cells. (PMID:24998916)
• LRIG3 functions as a tumor suppressor by attenuating EGFR signaling pathway. (PMID:25708990)
• LRIG3 plays an important role in Hela229 cell proliferation, apoptosis, and invasiveness. (PMID:26390694)
• This is the first time a haplotype on chromosome 12 containing sequence variants in the genes DCTN2, DNAH10, LRIG3, and MYO1A has been linked to an inherited neuropathy in humans. (PMID:26517670)
• Role of LRIG3 in cancer [review] (PMID:27628597)
• I these data of the current study indicated that overexpressed LRIG3 gene expression might inhibit the viability, adhesion, invasion and migration and promote the apoptosis of PC cells. (PMID:30412760)
• LRIG3 represses cell motility by inhibiting slug via inactivating ERK signaling in human colorectal cancer. (PMID:32107843)
• A novel circular RNA circ-LRIG3 facilitates the malignant progression of hepatocellular carcinoma by modulating the EZH2/STAT3 signaling. (PMID:33222697)
• miR-196a targeting LRIG3 promotes the proliferation and migration of cervical cancer cells. (PMID:33287939)
• LRIG proteins regulate lipid metabolism via BMP signaling and affect the risk of type 2 diabetes. (PMID:33469151)
• Prognostic significance of LRIG2 and LRIG3 proteins in urothelial bladder carcinoma. (PMID:34839782)
• Glioma-derived LRIG3 interacts with NETO2 in tumor-associated macrophages to modulate microenvironment and suppress tumor growth. (PMID:36639372)

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
		ENSDARG00000079363
mus_musculus	Lrig3	ENSMUSG00000020105
rattus_norvegicus	Lrig3	ENSRNOG00000007654
drosophila_melanogaster	Con	FBGN0005775
drosophila_melanogaster	kek3	FBGN0028370
caenorhabditis_elegans	lron-9	WBGENE00011971
caenorhabditis_elegans		WBGENE00020649

Paralogs (22): CHADL (ENSG00000100399), LGI1 (ENSG00000108231), LGR6 (ENSG00000133067), CHAD (ENSG00000136457), LGR5 (ENSG00000139292), LRIG1 (ENSG00000144749), LRRTM2 (ENSG00000146006), LRIT1 (ENSG00000148602), LGI2 (ENSG00000153012), LGI4 (ENSG00000153902), LRRC52 (ENSG00000162763), ELFN2 (ENSG00000166897), LGI3 (ENSG00000168481), LRG1 (ENSG00000171236), CPN2 (ENSG00000178772), LRIT3 (ENSG00000183423), LRRC26 (ENSG00000184709), LRIG2 (ENSG00000198799), LGR4 (ENSG00000205213), ELFN1 (ENSG00000225968), LRRC24 (ENSG00000254402), TRIL (ENSG00000255690)

Protein

Protein identifiers

Leucine-rich repeats and immunoglobulin-like domains protein 3 — Q6UXM1 (reviewed: Q6UXM1)

All UniProt accessions (4): C9K080, Q6UXM1, F8VYZ5, H0YID8

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in craniofacial and inner ear morphogenesis during embryonic development. May act within the otic vesicle epithelium to control formation of the lateral semicircular canal in the inner ear, possibly by restricting the expression of NTN1.

Subunit / interactions. Interacts with EGFR, ERBB2 and ERBB4 (in vitro).

Subcellular location. Cell membrane. Cytoplasmic vesicle membrane.

Tissue specificity. Widely expressed.

Isoforms (2)

UniProt ID	Names	Canonical?
Q6UXM1-1	1	yes
Q6UXM1-2	2

RefSeq proteins (2): NP_001129523, NP_700356* (*=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
IPR003598	Ig_sub2	Domain
IPR003599	Ig_sub	Domain
IPR007110	Ig-like_dom	Domain
IPR013098	Ig_I-set	Domain
IPR013783	Ig-like_fold	Homologous_superfamily
IPR032675	LRR_dom_sf	Homologous_superfamily
IPR036179	Ig-like_dom_sf	Homologous_superfamily
IPR050467	LRFN	Family

Pfam: PF00560, PF07679, PF13855, PF13927

UniProt features (41 total): repeat 15, glycosylation site 12, domain 5, disulfide bond 3, signal peptide 1, chain 1, transmembrane region 1, region of interest 1, compositionally biased region 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6UXM1-F1	73.40	0.51

Functional residue map

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

Disulfide bonds (3): 520–581, 624–676, 718–767

Glycosylation sites (12): 122, 156, 274, 442, 469, 515, 688, 729, 905, 987, 999, 1016

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 126 (showing top): GOBP_SENSORY_PERCEPTION_OF_MECHANICAL_STIMULUS, BILD_HRAS_ONCOGENIC_SIGNATURE, GOBP_ANIMAL_ORGAN_MORPHOGENESIS, GOBP_EAR_DEVELOPMENT, CADWELL_ATG16L1_TARGETS_DN, GOBP_EMBRYONIC_ORGAN_MORPHOGENESIS, GOBP_EAR_MORPHOGENESIS, GATA1_03, DOUGLAS_BMI1_TARGETS_DN, GOBP_SENSORY_PERCEPTION, GOBP_EMBRYO_DEVELOPMENT, GOBP_SENSORY_ORGAN_DEVELOPMENT, GOBP_SENSORY_ORGAN_MORPHOGENESIS, GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS, GOBP_EMBRYONIC_ORGAN_DEVELOPMENT

GO Biological Process (2): sensory perception of sound (GO:0007605), otolith morphogenesis (GO:0032474)

GO Molecular Function (2): signaling receptor activity (GO:0038023), protein binding (GO:0005515)

GO Cellular Component (5): obsolete extracellular space (GO:0005615), plasma membrane (GO:0005886), cytoplasmic vesicle membrane (GO:0030659), membrane (GO:0016020), cytoplasmic vesicle (GO:0031410)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
sensory perception of mechanical stimulus	1
inner ear morphogenesis	1
embryonic morphogenesis	1
otolith development	1
molecular transducer activity	1
binding	1
membrane	1
cell periphery	1
vesicle membrane	1
cytoplasmic vesicle	1
cellular anatomical structure	1
cytoplasm	1
intracellular vesicle	1

Protein interactions and networks

STRING

1377 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LRIG3	SLC34A2	O95436	743
LRIG3	KDELR2	P33947	731
LRIG3	ROS1	P08922	724
LRIG3	RET	P07949	691
LRIG3	GOPC	Q9HD26	650
LRIG3	SDC4	P31431	646
LRIG3	EGFR	P00533	644
LRIG3	TPM3	P06753	621
LRIG3	CD74	P04233	596
LRIG3	PTN	P21246	587
LRIG3	EZR	P15311	581
LRIG3	TPD52L1	Q16890	567
LRIG3	GML	Q99445	548
LRIG3	LIMA1	Q9UHB6	522
LRIG3	TMEM106B	Q9NUM4	509

IntAct

55 interactions, top by confidence:

A	B	Type	Score
LRIG1	LRIG3	psi-mi:“MI:0915”(physical association)	0.640
FBXO2	TMEM131L	psi-mi:“MI:0914”(association)	0.530
LRRC4C	DVL2	psi-mi:“MI:0914”(association)	0.530
CLGN	NPC1	psi-mi:“MI:0914”(association)	0.530
LRIG1	LRIG2	psi-mi:“MI:0914”(association)	0.530
GAL3ST1	NDUFA3	psi-mi:“MI:0914”(association)	0.530
SPSB2	ARHGEF10	psi-mi:“MI:0914”(association)	0.530
SPSB4	ARHGEF10	psi-mi:“MI:0914”(association)	0.530
CAND1	GTPBP10	psi-mi:“MI:0914”(association)	0.350
ERBB2	LRIG3	psi-mi:“MI:0914”(association)	0.350
	SHTN1	psi-mi:“MI:0914”(association)	0.350
HCN1	USP27X	psi-mi:“MI:0914”(association)	0.350
CACNA1C	SNRPGP15	psi-mi:“MI:0914”(association)	0.350
SYNGAP1	POM121C	psi-mi:“MI:0914”(association)	0.350
SYNGAP1	POTEF	psi-mi:“MI:0914”(association)	0.350
HCN1	POTEF	psi-mi:“MI:0914”(association)	0.350
CLEC12B	GXYLT2	psi-mi:“MI:0914”(association)	0.350
TMPRSS3	TMEM131L	psi-mi:“MI:0914”(association)	0.350
PDE3A	TMEM131L	psi-mi:“MI:0914”(association)	0.350

BioGRID (83): LRIG3 (Affinity Capture-MS), LRIG3 (Affinity Capture-MS), LRIG3 (Affinity Capture-MS), LRIG3 (Affinity Capture-MS), LRIG3 (Affinity Capture-MS), LRIG3 (Affinity Capture-MS), LRIG3 (Affinity Capture-MS), LRIG3 (Affinity Capture-MS), LRIG3 (Affinity Capture-MS), LRIG3 (Affinity Capture-MS), LRIG3 (Affinity Capture-MS), LRIG3 (Affinity Capture-MS), EGFR (Affinity Capture-Western), ERBB2 (Affinity Capture-Western), ERBB4 (Affinity Capture-Western)

ESM2 similar proteins: A6QLV3, A7SFP1, A8XWW4, B0W6M9, B3LWU3, B3P3E8, B4IBI9, B4JTV9, B4LXW1, B4N9T4, B4PU77, B4QVR7, B5DX45, B6CZ61, B9F655, O35125, O88520, Q1L8Y7, Q22875, Q32KP2, Q4R3P6, Q4V8I7, Q53EV4, Q5F4C4, Q5FVI3, Q5GIG6, Q5M8G4, Q5RAV5, Q5RFE9, Q5ZLN0, Q6AYI5, Q6DHL5, Q6GPJ5, Q6INV3, Q6P1C6, Q6UXM1, Q6ZVD8, Q7SXW3, Q7Z4L9, Q80VQ1

Diamond homologs: A0A087WV53, A1KZ92, A2AJ76, A4IFW2, A4IGL7, A6NDA9, B0BNK7, B0V2N1, D2HFT7, D3YXG0, D4A1J9, D4ABX8, F1NWE3, G5EG78, O15146, O73775, O75325, O94898, P07722, P15364, P20916, P20917, P23468, P43146, P48960, P53813, P70193, P70211, Q03142, Q08761, Q08879, Q13332, Q13449, Q1ENI8, Q1RMS4, Q1WIM1, Q21038, Q24372, Q26474, Q2Q421

SIGNOR signaling

3 interactions.

A	Effect	B	Mechanism
LRIG1	down-regulates	LRIG3
LRIG3	up-regulates	ERBB2
LRIG3	up-regulates	ERBB4

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 68 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
SLC-mediated transmembrane transport	7	9.4×	2e-03

Disease & clinical

Cancer significance

From intOGen — cancer-driver classification: loss-of-function (tumor-suppressor-like) across 1 cancer types — BLCA.

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	124
Likely benign	8
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

3348 predictions. Top by Δscore:

Variant	Effect	Δscore
12:58872813:GTACC:G	acceptor_loss	1.0000
12:58872815:ACC:A	acceptor_loss	1.0000
12:58872816:CCTG:C	acceptor_loss	1.0000
12:58872818:T:C	acceptor_loss	1.0000
12:58874184:T:TA	donor_gain	1.0000
12:58874485:AGGG:A	donor_gain	1.0000
12:58874572:CCCTT:C	acceptor_gain	1.0000
12:58874573:CCTT:C	acceptor_gain	1.0000
12:58876444:CCA:C	donor_gain	1.0000
12:58877397:CA:C	donor_loss	1.0000
12:58877399:C:CT	donor_loss	1.0000
12:58877848:TGTTT:T	acceptor_gain	1.0000
12:58877850:TTT:T	acceptor_gain	1.0000
12:58877851:TT:T	acceptor_gain	1.0000
12:58877852:TCTGA:T	acceptor_loss	1.0000
12:58877853:C:CC	acceptor_gain	1.0000
12:58877853:CTG:C	acceptor_loss	1.0000
12:58877854:T:C	acceptor_loss	1.0000
12:58878858:T:TA	donor_gain	1.0000
12:58878859:C:A	donor_gain	1.0000
12:58879103:GCA:G	acceptor_gain	1.0000
12:58879104:CA:C	acceptor_gain	1.0000
12:58879104:CAC:C	acceptor_gain	1.0000
12:58879106:C:CC	acceptor_gain	1.0000
12:58880579:A:AC	donor_gain	1.0000
12:58880580:C:CC	donor_gain	1.0000
12:58880586:A:AC	donor_gain	1.0000
12:58880587:C:CC	donor_gain	1.0000
12:58880641:A:AC	donor_gain	1.0000
12:58880642:C:CC	donor_gain	1.0000

AlphaMissense

7379 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:58877681:A:G	L752P	1.000
12:58877746:C:A	W730C	1.000
12:58877746:C:G	W730C	1.000
12:58877748:A:G	W730R	1.000
12:58877748:A:T	W730R	1.000
12:58878835:A:G	L691P	1.000
12:58878867:G:C	N680K	1.000
12:58878867:G:T	N680K	1.000
12:58878898:T:A	D670V	1.000
12:58878999:C:A	W636C	1.000
12:58878999:C:G	W636C	1.000
12:58879001:A:G	W636R	1.000
12:58879001:A:T	W636R	1.000
12:58880780:C:A	W534C	1.000
12:58880780:C:G	W534C	1.000
12:58880782:A:G	W534R	1.000
12:58880782:A:T	W534R	1.000
12:58877591:A:G	L782P	0.999
12:58877623:G:C	N771K	0.999
12:58877623:G:T	N771K	0.999
12:58877637:A:G	C767R	0.999
12:58877642:T:C	Y765C	0.999
12:58877642:T:G	Y765S	0.999
12:58877643:A:C	Y765D	0.999
12:58877649:C:A	G763W	0.999
12:58877747:C:G	W730S	0.999
12:58877784:A:G	C718R	0.999
12:58877789:A:G	L716P	0.999
12:58878829:A:T	V693D	0.999
12:58878842:C:G	A689P	0.999

dbSNP variants (sampled 300 via entrez): RS1000099126 (12:58910385 G>A), RS1000170081 (12:58881805 G>A), RS1000219930 (12:58875321 C>A,G,T), RS1000396533 (12:58887309 G>A), RS1000455741 (12:58881526 G>A), RS1000474351 (12:58873222 C>T), RS1000509352 (12:58880191 G>A), RS1000517063 (12:58920616 G>A,T), RS1000612716 (12:58914743 C>A,T), RS1000626215 (12:58921913 G>A), RS1000628215 (12:58913659 C>G,T), RS1000696748 (12:58914854 TGA>T), RS1000737449 (12:58886687 T>A,C), RS1000790356 (12:58880090 T>A,C), RS1000794079 (12:58888063 G>C)

Disease associations

OMIM: gene MIM:608870 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST000675_11	Heart failure	7.000000e-08
GCST002450_9	Plasma omega-6 polyunsaturated fatty acid levels (gamma-linolenic acid)	8.000000e-07
GCST005994_13	Hematocrit	4.000000e-08
GCST006585_878	Blood protein levels	2.000000e-26

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0005680	omega-6 polyunsaturated fatty acid measurement
EFO:0004348	hematocrit

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
rs7970054	LRIG3		0.00	0

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, decreases methylation	6
trichostatin A	affects cotreatment, decreases expression	3
sodium arsenite	affects cotreatment, increases abundance, decreases expression	2
Cadmium Chloride	decreases expression	2
aristolochic acid I	decreases expression	1
urushiol	increases expression	1
bisphenol A	decreases expression	1
terbufos	increases methylation	1
cobaltous chloride	decreases expression	1
zinc chromate	increases abundance, increases expression	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
potassium chromate(VI)	decreases expression	1
nickel sulfate	increases expression	1
resorcinol	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
chromium hexavalent ion	increases abundance, increases expression	1
perfluorooctane sulfonic acid	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine	increases expression, increases response to substance	1
NSC 689534	affects binding, decreases expression	1
Leflunomide	increases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	affects cotreatment, decreases expression, increases abundance	1
Benzo(a)pyrene	decreases expression	1
Calcitriol	decreases expression	1
Copper	affects binding, decreases expression	1
Doxorubicin	decreases expression	1
Fonofos	increases methylation	1

Clinical trials (associated diseases)

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