LIN7C

Summary

LIN7C (lin-7 cell polarity scaffold C, HGNC:17789) is a protein-coding gene on chromosome 11p14.1, encoding Protein lin-7 homolog C (Q9NUP9). Plays a role in establishing and maintaining the asymmetric distribution of channels and receptors at the plasma membrane of polarized cells.

Enables L27 domain binding activity and cytoskeletal protein binding activity. Involved in morphogenesis of an epithelial sheet. Located in cell-cell junction; cytoplasm; and plasma membrane. Part of MPP7-DLG1-LIN7 complex.

Source: NCBI Gene 55327 — RefSeq curated summary.

At a glance

• GWAS associations: 13
• Clinical variants (ClinVar): 23 total
• MANE Select transcript: NM_018362

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:17789
Approved symbol	LIN7C
Name	lin-7 cell polarity scaffold C
Location	11p14.1
Locus type	gene with protein product
Status	Approved
Aliases	MALS-3, LIN-7C, LIN-7-C, VELI3, FLJ11215
Ensembl gene	ENSG00000148943
Ensembl biotype	protein_coding
OMIM	612332
Entrez	55327

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000278193, ENST00000524596

RefSeq mRNA: 1 — MANE Select: NM_018362 NM_018362

CCDS: CCDS7864

Canonical transcript exons

ENST00000278193 — 5 exons

Exon	Start	End
ENSE00000988213	27501495	27501566
ENSE00001215645	27501802	27501920
ENSE00001215658	27494418	27498804
ENSE00001363619	27499359	27499568
ENSE00001363638	27506716	27506769

Expression profiles

Bgee: expression breadth ubiquitous, 291 present calls, max score 98.60.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 26.2637 / max 904.2777, expressed in 1800 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
119072	24.0290	1795
119068	1.8684	991
119069	0.3375	141
119067	0.0287	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
esophagus squamous epithelium	UBERON:0006920	98.60	gold quality
choroid plexus epithelium	UBERON:0003911	97.82	gold quality
germinal epithelium of ovary	UBERON:0001304	97.58	gold quality
epithelium of nasopharynx	UBERON:0001951	97.23	gold quality
pigmented layer of retina	UBERON:0001782	97.16	gold quality
retina	UBERON:0000966	97.13	gold quality
tibia	UBERON:0000979	96.79	gold quality
squamous epithelium	UBERON:0006914	96.48	gold quality
blood vessel layer	UBERON:0004797	96.30	gold quality
oral cavity	UBERON:0000167	96.12	gold quality
Brodmann (1909) area 23	UBERON:0013554	96.11	gold quality
visceral pleura	UBERON:0002401	96.10	gold quality
epithelium of esophagus	UBERON:0001976	96.09	gold quality
parietal pleura	UBERON:0002400	96.02	gold quality
nephron tubule	UBERON:0001231	95.93	gold quality
gingival epithelium	UBERON:0001949	95.92	gold quality
mucosa of sigmoid colon	UBERON:0004993	95.86	gold quality
seminal vesicle	UBERON:0000998	95.75	gold quality
secondary oocyte	CL:0000655	95.63	gold quality
endothelial cell	CL:0000115	95.61	gold quality
renal glomerulus	UBERON:0000074	95.56	gold quality
gingiva	UBERON:0001828	95.54	gold quality
superficial temporal artery	UBERON:0001614	95.42	gold quality
colonic mucosa	UBERON:0000317	95.39	gold quality
mucosa of paranasal sinus	UBERON:0005030	95.38	gold quality
metanephric glomerulus	UBERON:0004736	95.37	gold quality
jejunal mucosa	UBERON:0000399	95.32	gold quality
parotid gland	UBERON:0001831	95.22	gold quality
corpus epididymis	UBERON:0004359	95.12	gold quality
pleura	UBERON:0000977	94.97	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.35

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

221 targeting LIN7C, 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-3646	100.00	73.56	5283
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-433-3P	99.98	69.37	1203
HSA-MIR-548P	99.98	72.25	3784

Literature-anchored findings (GeneRIF, showing 6)

• analysis of the solution structure of the heterodimer composed of the L27 domains from LIN-2 and LIN-7 (PMID:16147993)
• LIN7C is a PDZ protein that interacts with human papillomavirus-16 E6 and forms a tripartite complex with MPP7 and DLG1, regulating the stability and localization of DLG1 to cell junctions. (PMID:17237226)
• Overexpression of the Lin-7C gene in an OSCC cell clone does not contribute to underproliferation but results in a noninvasive phenotype with elevated beta-catenin expression. (PMID:17942893)
• Allelic and haplotype association was found between both BDNF and adult ADHD, and LIN-7 and adult ADHD. (PMID:18286632)
• The Dlg1-MPP7-Mals3 heterotrimer consists of 2 pairs of heterodimeric L27 domains. These 2 dimers are asymmetric due to the large difference between the N- and C-terminal tandem L27 domain of MPP7. (PMID:20702775)
• Data show that mirtazapine caused substantial up-regulation of the Lin-7C/beta-catenin pathway in a metastatic squamous cell carcinomas (hSCCs) cell line and melanoma-derived cell line. (PMID:24961284)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
mus_musculus	Lin7c	ENSMUSG00000027162
rattus_norvegicus	Lin7c	ENSRNOG00000062543
drosophila_melanogaster	veli	FBGN0039269
caenorhabditis_elegans		WBGENE00002996

Paralogs (3): LIN7B (ENSG00000104863), LIN7A (ENSG00000111052), PDZD11 (ENSG00000120509)

Protein

Protein identifiers

Protein lin-7 homolog C — Q9NUP9 (reviewed: Q9NUP9)

Alternative names: Mammalian lin-seven protein 3, Vertebrate lin-7 homolog 3

All UniProt accessions (2): Q9NUP9, G3V1D4

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in establishing and maintaining the asymmetric distribution of channels and receptors at the plasma membrane of polarized cells. Forms membrane-associated multiprotein complexes that may regulate delivery and recycling of proteins to the correct membrane domains. The tripartite complex composed of LIN7 (LIN7A, LIN7B or LIN7C), CASK and APBA1 associates with the motor protein KIF17 to transport vesicles containing N-methyl-D-aspartate (NMDA) receptor subunit NR2B along microtubules. This complex may have the potential to couple synaptic vesicle exocytosis to cell adhesion in brain. Ensures the proper localization of GRIN2B (subunit 2B of the NMDA receptor) to neuronal postsynaptic density and may function in localizing synaptic vesicles at synapses where it is recruited by beta-catenin and cadherin. Required to localize Kir2 channels, GABA transporter (SLC6A12) and EGFR/ERBB1, ERBB2, ERBB3 and ERBB4 to the basolateral membrane of epithelial cells.

Subunit / interactions. Forms a complex with CASK and APBA1 or CASKIN1. Component of the brain-specific heterotrimeric complex (LIN-10-LIN-2-LIN-7 complex) composed of at least APBA1, CASK, and LIN7, which associates with the motor protein KIF17 to transport vesicles along microtubules. Can also interact with other modular proteins containing protein-protein interaction domains like PALS1, PALS2, MPP7, DLG1, DLG2 and DLG3 through its L27 domain. Interacts with DLG4 and GRIN2B as well as CDH1 and CTNNB1, the channels KCNJ12/Kir2.2, KCNJ4/Kir2.3 and probably KCNJ2/Kir2.1 and SLC6A12/BGT-1 via its PDZ domain. The association of LIN7A with cadherin and beta-catenin is calcium-dependent, occurs at synaptic junctions and requires the actin cytoskeleton. Interacts with EGFR, ERBB2, ERBB3 and ERBB4 with both PDZ and KID domains. Associates with KIF17 via APBA1. Interacts with HTR4. Forms a tripartite complex composed of DLG1, MPP7 and LIN7 (LIN7A or LIN7C). Interacts with MAPK12. (Microbial infection) Interacts with DLG1; DLG1 acts as a scaffold protein that facilitates the interaction between LIN7C and influenza A virus protein NS1; the interaction facilitates translocation of LIN7C to cytoplasmic puncta.

Subcellular location. Cell membrane. Basolateral cell membrane. Cell junction. Postsynaptic density membrane. Tight junction.

Domain organisation. The kinase interacting site is required for proper delivery of ERBB2 to the basolateral membrane. The PDZ domain regulates endocytosis and recycling of the receptor at the membrane. The L27 domain mediates interaction with CASK and is involved in the formation of multimeric complexes and the association of LIN7 to membranes.

Similarity. Belongs to the lin-7 family.

RefSeq proteins (1): NP_060832* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001478	PDZ	Domain
IPR004172	L27_dom	Domain
IPR014775	L27_C	Domain
IPR017365	LIN7	Family
IPR036034	PDZ_sf	Homologous_superfamily
IPR036892	L27_dom_sf	Homologous_superfamily
IPR051109	MAM_complex_regulator	Family

Pfam: PF00595, PF02828

UniProt features (9 total): helix 3, domain 2, initiator methionine 1, chain 1, short sequence motif 1, modified residue 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
3LRA	X-RAY DIFFRACTION	2.95

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NUP9-F1	87.60	0.47

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): 2

Function

Pathways and Gene Ontology

Reactome pathways

9 pathways

ID	Pathway
R-HSA-212676	Dopamine Neurotransmitter Release Cycle
R-HSA-6794361	Neurexins and neuroligins
R-HSA-9609736	Assembly and cell surface presentation of NMDA receptors
R-HSA-112310	Neurotransmitter release cycle
R-HSA-112314	Neurotransmitter receptors and postsynaptic signal transmission
R-HSA-112315	Transmission across Chemical Synapses
R-HSA-112316	Neuronal System
R-HSA-442755	Activation of NMDA receptors and postsynaptic events
R-HSA-6794362	Protein-protein interactions at synapses

MSigDB gene sets: 221 (showing top): GOBP_NEUROMUSCULAR_JUNCTION_DEVELOPMENT, GOBP_MORPHOGENESIS_OF_AN_EPITHELIUM, GOBP_SYNAPTIC_VESICLE_LOCALIZATION, GOBP_EPITHELIUM_DEVELOPMENT, HORIUCHI_WTAP_TARGETS_DN, GOBP_VESICLE_LOCALIZATION, GOBP_SYNAPSE_ASSEMBLY, GOBP_REGULATION_OF_DEVELOPMENTAL_GROWTH, GOBP_GROWTH, GOBP_NEUROTRANSMITTER_TRANSPORT, GOBP_REGULATION_OF_CELL_JUNCTION_ASSEMBLY, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_CELL_CELL_SIGNALING, GOBP_EXOCYTOSIS

GO Biological Process (6): morphogenesis of an epithelial sheet (GO:0002011), exocytosis (GO:0006887), neurotransmitter secretion (GO:0007269), regulation of synaptic assembly at neuromuscular junction (GO:0008582), protein transport (GO:0015031), synaptic vesicle transport (GO:0048489)

GO Molecular Function (6): cytoskeletal protein binding (GO:0008092), protein domain specific binding (GO:0019904), PDZ domain binding (GO:0030165), protein-macromolecule adaptor activity (GO:0030674), L27 domain binding (GO:0097016), protein binding (GO:0005515)

GO Cellular Component (13): cytoplasm (GO:0005737), plasma membrane (GO:0005886), cell-cell junction (GO:0005911), bicellular tight junction (GO:0005923), basolateral plasma membrane (GO:0016323), synapse (GO:0045202), MPP7-DLG1-LIN7 complex (GO:0097025), presynapse (GO:0098793), postsynaptic density membrane (GO:0098839), glutamatergic synapse (GO:0098978), membrane (GO:0016020), postsynaptic membrane (GO:0045211), anchoring junction (GO:0070161)

Reactome top-level categories

Rollup of top-6 pathways:

Category	Pathways
Transmission across Chemical Synapses	2
Neuronal System	2
Neurotransmitter release cycle	1
Protein-protein interactions at synapses	1
Activation of NMDA receptors and postsynaptic events	1
Neurotransmitter receptors and postsynaptic signal transmission	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
protein binding	3
cellular anatomical structure	3
transport	2
protein domain specific binding	2
cell junction	2
synapse	2
morphogenesis of an epithelium	1
vesicle-mediated transport	1
secretion by cell	1
vesicle fusion to plasma membrane	1
neurotransmitter transport	1
chemical synaptic transmission	1
establishment of localization in cell	1
presynapse	1
signal release from synapse	1
regulation of developmental growth	1
synaptic assembly at neuromuscular junction	1
regulation of synapse assembly	1
regulation of neuromuscular junction development	1
intracellular protein localization	1
establishment of protein localization	1
cellular process	1
establishment of vesicle localization	1
synaptic vesicle localization	1
molecular adaptor activity	1
binding	1
intracellular anatomical structure	1
membrane	1
cell periphery	1
anchoring junction	1
apical junction complex	1
tight junction	1
basal plasma membrane	1
plasma membrane region	1
adherens junction	1
plasma membrane protein complex	1
postsynaptic density	1
postsynaptic membrane	1
postsynaptic specialization membrane	1
synaptic membrane	1

Protein interactions and networks

STRING

1018 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LIN7C	APBA1	Q02410	902
LIN7C	PALS1	Q8N3R9	874
LIN7C	MARCHF11	A6NNE9	839
LIN7C	DLG4	P78352	829
LIN7C	CASK	O14936	826
LIN7C	PATJ	Q8NI35	803
LIN7C	CRB3	Q9BUF7	797
LIN7C	MPP3	Q13368	726
LIN7C	NCR3	O14931	647
LIN7C	CCDC34	Q96HJ3	618
LIN7C	MPP2	Q14168	583
LIN7C	LGR4	Q9BXB1	560
LIN7C	KCNA3	P22001	555
LIN7C	PALS2	Q9NZW5	549
LIN7C	GRK7	Q8WTQ7	549

IntAct

515 interactions, top by confidence:

A	B	Type	Score
PALS1	LIN7A	psi-mi:“MI:0914”(association)	0.870
PALS1	LIN7C	psi-mi:“MI:0915”(physical association)	0.800
MPP7	LIN7C	psi-mi:“MI:0915”(physical association)	0.800
LIN7C	PALS2	psi-mi:“MI:0915”(physical association)	0.800
MPP3	LIN7C	psi-mi:“MI:0915”(physical association)	0.740
KCNJ2	KCNJ18	psi-mi:“MI:2364”(proximity)	0.660
MPP2	LIN7A	psi-mi:“MI:0914”(association)	0.640
SLC20A1	LIN7A	psi-mi:“MI:0914”(association)	0.640
LIN7C	HTR2C	psi-mi:“MI:0915”(physical association)	0.590
CYSLTR2	CASK	psi-mi:“MI:0914”(association)	0.590
DLGAP4	LIN7A	psi-mi:“MI:0914”(association)	0.590
APBA1	LIN7A	psi-mi:“MI:0914”(association)	0.590
CYSLTR2	LIN7C	psi-mi:“MI:0407”(direct interaction)	0.590
EPHA7	LIN7C	psi-mi:“MI:0407”(direct interaction)	0.570
MPP2	LIN7C	psi-mi:“MI:0915”(physical association)	0.560
YES1	LIN7C	psi-mi:“MI:0915”(physical association)	0.560
NSUN2	LIN7A	psi-mi:“MI:0914”(association)	0.530
SPATA2	CASK	psi-mi:“MI:0914”(association)	0.530
LIN7C	ABLIM1	psi-mi:“MI:0914”(association)	0.530
SLC31A1	C2orf72	psi-mi:“MI:0914”(association)	0.530
MPP2	ABLIM1	psi-mi:“MI:0914”(association)	0.530
C1orf174	AHCYL1	psi-mi:“MI:0914”(association)	0.530
PALS1	AMOTL1	psi-mi:“MI:0914”(association)	0.530

BioGRID (212): LIN7C (Affinity Capture-MS), LIN7C (Affinity Capture-MS), LIN7C (Affinity Capture-MS), MPDZ (Affinity Capture-MS), INADL (Affinity Capture-MS), MPP2 (Affinity Capture-MS), MPP6 (Affinity Capture-MS), ABLIM1 (Affinity Capture-MS), MPP7 (Affinity Capture-MS), MPP3 (Affinity Capture-MS), DLG1 (Affinity Capture-MS), KIF26B (Affinity Capture-MS), MPP5 (Affinity Capture-MS), LIN7B (Affinity Capture-MS), CASK (Affinity Capture-MS)

ESM2 similar proteins: A8MUH7, B1AK53, D2I3C6, O14745, O14976, O15085, O35071, O35787, O43896, O70145, O77775, O88951, O88952, P00520, P00521, P19838, P19878, P70271, P70441, P98150, Q00653, Q0P5F3, Q15599, Q28619, Q2KIB6, Q3SZK8, Q4L1J4, Q4R6G4, Q570Y9, Q5F425, Q5RAA5, Q5RC07, Q5ZM14, Q63618, Q6RHR9, Q792I0, Q8C033, Q8SQG9, Q8TB45, Q920G2

Diamond homologs: A0A140LI67, A5PKA5, A7UA95, E1JIT7, O14910, O15018, O19132, O35274, O35867, O35889, O62666, O62674, O62675, O62676, O62677, O62678, O88951, O88952, P11434, P29475, P29476, P31016, P51140, P55196, P57105, P78352, Q07436, Q0P5F3, Q12923, Q14005, Q29498, Q2KIB6, Q32LM6, Q3T0C9, Q3UHD6, Q4KL35, Q5F425, Q5RAA5, Q62108, Q64512

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
LIN7C	“form complex”	AMOT/MPP5/INADL/LIN7C	binding
LIN7C	“form complex”	“CASK-Mint1-Veli complex”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 182 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
Assembly and cell surface presentation of NMDA receptors	6	11.7×	7e-03
EPH-ephrin mediated repulsion of cells	6	10.1×	8e-03
Neurexins and neuroligins	6	9.1×	8e-03
R-HSA-425366	6	8.4×	8e-03
RHOA GTPase cycle	9	5.2×	8e-03
SLC-mediated transmembrane transport	10	4.5×	8e-03

GO biological processes:

GO term	Partners	Fold	FDR
ephrin receptor signaling pathway	6	13.0×	4e-03
regulation of small GTPase mediated signal transduction	9	8.2×	2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	16
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

792 predictions. Top by Δscore:

Variant	Effect	Δscore
11:27499352:T:TA	donor_gain	1.0000
11:27499353:CCTTA:C	donor_loss	1.0000
11:27499354:CTTA:C	donor_loss	1.0000
11:27499356:TAC:T	donor_loss	1.0000
11:27499356:TACC:T	donor_gain	1.0000
11:27499357:A:AC	donor_gain	1.0000
11:27499357:AC:A	donor_gain	1.0000
11:27499357:ACC:A	donor_loss	1.0000
11:27499357:ACCA:A	donor_gain	1.0000
11:27499358:C:CC	donor_gain	1.0000
11:27499358:C:CT	donor_gain	1.0000
11:27499358:CC:C	donor_gain	1.0000
11:27499358:CCA:C	donor_gain	1.0000
11:27499358:CCACT:C	donor_gain	1.0000
11:27499564:GTAGC:G	acceptor_gain	1.0000
11:27499565:TAGC:T	acceptor_gain	1.0000
11:27499566:AGC:A	acceptor_gain	1.0000
11:27499567:GC:G	acceptor_gain	1.0000
11:27499568:CC:C	acceptor_gain	1.0000
11:27499569:C:CA	acceptor_loss	1.0000
11:27499569:C:CC	acceptor_gain	1.0000
11:27501490:TTTA:T	donor_gain	1.0000
11:27501493:AC:A	donor_loss	1.0000
11:27501494:C:A	donor_loss	1.0000
11:27501562:TATAC:T	acceptor_gain	1.0000
11:27501563:ATAC:A	acceptor_gain	1.0000
11:27501564:TAC:T	acceptor_gain	1.0000
11:27501567:C:CA	acceptor_loss	1.0000
11:27501568:T:G	acceptor_loss	1.0000
11:27501798:TCA:T	donor_loss	1.0000

AlphaMissense

1268 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:27498737:A:G	L169S	1.000
11:27498764:A:G	L160P	1.000
11:27499369:A:T	V143D	1.000
11:27499373:A:G	S142P	1.000
11:27499378:A:T	L140H	1.000
11:27499384:T:A	D138V	1.000
11:27499384:T:C	D138G	1.000
11:27499384:T:G	D138A	1.000
11:27499387:C:T	G137E	1.000
11:27499396:A:T	L134H	1.000
11:27499414:G:T	A128D	1.000
11:27499441:A:C	I119R	1.000
11:27499441:A:T	I119K	1.000
11:27499471:C:T	G109E	1.000
11:27499472:C:G	G109R	1.000
11:27499472:C:T	G109R	1.000
11:27499477:A:T	I107N	1.000
11:27499483:A:G	F105S	1.000
11:27499486:C:A	G104V	1.000
11:27499486:C:T	G104E	1.000
11:27499487:C:G	G104R	1.000
11:27499487:C:T	G104R	1.000
11:27498731:A:T	V171E	0.999
11:27498764:A:T	L160Q	0.999
11:27498767:A:G	L159P	0.999
11:27498776:G:T	A156D	0.999
11:27498786:G:C	H153D	0.999
11:27498800:A:T	V148D	0.999
11:27499365:A:C	N144K	0.999
11:27499365:A:T	N144K	0.999

dbSNP variants (sampled 300 via entrez): RS1000276094 (11:27496290 G>A), RS1000403364 (11:27495073 C>T), RS1000836613 (11:27499954 T>C), RS1001074292 (11:27506208 G>A), RS1001422200 (11:27506354 A>T), RS1001521605 (11:27494532 T>C), RS1001750269 (11:27500918 T>C), RS1001761942 (11:27494176 A>G), RS1001795083 (11:27504527 A>C), RS1001880740 (11:27499700 G>T), RS1001933210 (11:27499878 T>C), RS1002188352 (11:27506157 G>A), RS1003019134 (11:27497299 T>C), RS1003528651 (11:27506152 C>T), RS1003716035 (11:27494970 T>C)

Disease associations

OMIM: gene MIM:612332 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

13 associations (top):

Study	Trait	p-value
GCST001482_3	Lumbar spine bone mineral density	5.000000e-08
GCST002493_1	Bone mineral density (paediatric, skull)	8.000000e-06
GCST002493_7	Bone mineral density (paediatric, skull)	2.000000e-17
GCST002493_8	Bone mineral density (paediatric, skull)	3.000000e-13
GCST003993_40	Menarche (age at onset)	1.000000e-09
GCST004066_10	Hip circumference	2.000000e-07
GCST004066_112	Hip circumference	1.000000e-09
GCST004485_13	Survival in pancreatic cancer	1.000000e-06
GCST006943_6	Feeling miserable	6.000000e-09
GCST006948_59	Feeling nervous	3.000000e-09
GCST007565_61	Morning person	3.000000e-15
GCST007576_358	Chronotype	3.000000e-15
GCST010703_169	Brain morphology (MOSTest)	5.000000e-09

EFO canonical traits (6, from GWAS)

EFO ID	Trait name
EFO:0004703	age at menarche
EFO:0000638	overall survival
EFO:0009598	feeling miserable measurement
EFO:0009597	feeling nervous measurement
EFO:0008328	chronotype 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

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects methylation, decreases expression	2
GSK-J4	increases expression	1
methylparaben	increases expression	1
nickel chloride	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
ICG 001	decreases expression	1
jinfukang	decreases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Arsenic Trioxide	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Cisplatin	decreases expression	1
Cocaine	increases expression	1
Coumestrol	increases expression	1
Doxorubicin	decreases expression	1
Enzyme Inhibitors	increases O-linked glycosylation, decreases activity	1
Hydrogen Peroxide	affects expression	1
Ivermectin	decreases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Sarin	increases expression	1
Thimerosal	increases expression	1
Tobacco Smoke Pollution	affects expression	1
Tretinoin	decreases expression	1
Valproic Acid	increases expression	1
Aflatoxin M1	decreases expression	1
Lactic Acid	decreases expression	1
Topotecan	affects response to substance	1
Particulate Matter	decreases expression, increases abundance	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_B1VU	Abcam HeLa LIN7C KO	Cancer cell line	Female

Clinical trials (associated diseases)

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