LIN7A

Summary

LIN7A (lin-7 cell polarity scaffold A, HGNC:17787) is a protein-coding gene on chromosome 12q21.31, encoding Protein lin-7 homolog A (O14910). Plays a role in establishing and maintaining the asymmetric distribution of channels and receptors at the plasma membrane of polarized cells.

The protein encoded by this gene is involved in generating and maintaining the asymmetric distribution of channels and receptors at the cell membrane. The encoded protein also is required for the localization of some specific channels and can be part of a protein complex that couples synaptic vesicle exocytosis to cell adhesion in the brain.

Source: NCBI Gene 8825 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 38 total — 2 pathogenic, 1 likely-pathogenic
• MANE Select transcript: NM_004664

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:17787
Approved symbol	LIN7A
Name	lin-7 cell polarity scaffold A
Location	12q21.31
Locus type	gene with protein product
Status	Approved
Aliases	MALS-1, TIP-33, LIN-7A, VELI1
Ensembl gene	ENSG00000111052
Ensembl biotype	protein_coding
OMIM	603380
Entrez	8825

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 5 protein_coding, 1 nonsense_mediated_decay

ENST00000261203, ENST00000549417, ENST00000552093, ENST00000552864, ENST00000877321, ENST00000877322

RefSeq mRNA: 2 — MANE Select: NM_004664 NM_001324423, NM_004664

CCDS: CCDS9021

Canonical transcript exons

ENST00000552864 — 6 exons

Exon	Start	End
ENSE00000752681	80848251	80848322
ENSE00000937496	80889251	80889369
ENSE00001164545	80937641	80937934
ENSE00002391409	80792520	80797726
ENSE00003618882	80811465	80811683
ENSE00003657812	80845730	80845939

Expression profiles

Bgee: expression breadth ubiquitous, 222 present calls, max score 94.53.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.6743 / max 1141.5262, expressed in 1259 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter ID	TPM avg	Samples expressed
132295	9.8432	1164
132300	3.5048	671
132296	2.4582	826
132299	0.4673	179
132301	0.2077	104
132297	0.0986	43
132298	0.0652	23
132302	0.0194	3
132303	0.0077	3
132304	0.0022	1

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
Brodmann (1909) area 23	UBERON:0013554	94.53	gold quality
endothelial cell	CL:0000115	92.21	silver quality
middle temporal gyrus	UBERON:0002771	92.13	gold quality
pigmented layer of retina	UBERON:0001782	91.54	gold quality
primary visual cortex	UBERON:0002436	88.70	gold quality
cortical plate	UBERON:0005343	87.33	gold quality
trabecular bone tissue	UBERON:0002483	87.30	gold quality
blood	UBERON:0000178	86.85	gold quality
cerebellar cortex	UBERON:0002129	86.63	gold quality
cerebellar hemisphere	UBERON:0002245	86.60	gold quality
entorhinal cortex	UBERON:0002728	85.90	gold quality
bone marrow	UBERON:0002371	85.70	gold quality
right hemisphere of cerebellum	UBERON:0014890	85.58	gold quality
cerebellum	UBERON:0002037	85.56	gold quality
postcentral gyrus	UBERON:0002581	85.12	gold quality
occipital lobe	UBERON:0002021	84.64	gold quality
monocyte	CL:0000576	84.35	gold quality
superior frontal gyrus	UBERON:0002661	84.34	gold quality
mononuclear cell	CL:0000842	84.03	gold quality
left testis	UBERON:0004533	83.97	gold quality
leukocyte	CL:0000738	83.51	gold quality
lateral nuclear group of thalamus	UBERON:0002736	83.47	gold quality
right lobe of liver	UBERON:0001114	83.45	gold quality
parietal lobe	UBERON:0001872	83.42	gold quality
right testis	UBERON:0004534	82.61	gold quality
testis	UBERON:0000473	82.42	gold quality
liver	UBERON:0002107	82.41	gold quality
sperm	CL:0000019	81.80	gold quality
substantia nigra pars reticulata	UBERON:0001966	81.29	gold quality
body of uterus	UBERON:0009853	81.09	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-7316	yes	31.17
E-ANND-3	yes	5.13

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

243 targeting LIN7A, 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-1277-5P	100.00	73.95	5056
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996

Literature-anchored findings (GeneRIF, showing 7)

• coordinated folding and association of the LIN-2, -7 domain (PMID:12110687)
• LIN7A 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)
• Allelic and haplotype association was found between both BDNF and adult ADHD, and LIN-7 and adult ADHD. (PMID:18286632)
• LIN7A depletion disrupts cerebral cortex development, contributing to intellectual disability in 12q21-deletion syndrome. (PMID:24658322)
• This study therefore shows that LIN7A has a crucial role in the polarity abnormalities associated with breast carcinogenesis. (PMID:26887652)
• Overexpression of LIN7 or IRSp53 did not prevent the formation of hyperfused mitochondria in cells coexpressing the Drp1 K38A mutant, thus suggesting that LIN7-IRSp53 complex requires functional Drp1 to regulate mitochondrial morphology. (PMID:27320196)
• miR-501-3p suppresses metastasis and progression of hepatocellular carcinoma through targeting LIN7A. (PMID:29749382)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	lin7a	ENSDARG00000013414
mus_musculus	Lin7a	ENSMUSG00000019906
rattus_norvegicus	Lin7a	ENSRNOG00000004527
drosophila_melanogaster	veli	FBGN0039269
caenorhabditis_elegans		WBGENE00002996

Paralogs (3): LIN7B (ENSG00000104863), PDZD11 (ENSG00000120509), LIN7C (ENSG00000148943)

Protein

Protein identifiers

Protein lin-7 homolog A — O14910 (reviewed: O14910)

Alternative names: Mammalian lin-seven protein 1, Tax interaction protein 33, Vertebrate lin-7 homolog 1

All UniProt accessions (4): O14910, H0YI92, H0YIA8, J3KN23

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 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, GRIN2B and MARCHF11 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).

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

Tissue specificity. Expressed in brain, testis, kidney, placenta and liver.

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 (2): NP_001311352, NP_004655* (*=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 (5 total): domain 2, chain 1, short sequence motif 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O14910-F1	80.84	0.44

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: 219 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_UP, GOBP_NEUROMUSCULAR_JUNCTION_DEVELOPMENT, GOBP_SYNAPTIC_VESICLE_LOCALIZATION, GOBP_VESICLE_LOCALIZATION, GOBP_SYNAPSE_ASSEMBLY, GOBP_REGULATION_OF_DEVELOPMENTAL_GROWTH, GOZGIT_ESR1_TARGETS_DN, 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, GOBP_CELL_JUNCTION_ORGANIZATION

GO Biological Process (7): 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), inner ear development (GO:0048839), protein-containing complex assembly (GO:0065003)

GO Molecular Function (3): protein-macromolecule adaptor activity (GO:0030674), L27 domain binding (GO:0097016), protein binding (GO:0005515)

GO Cellular Component (12): plasma membrane (GO:0005886), cell-cell junction (GO:0005911), bicellular tight junction (GO:0005923), basolateral plasma membrane (GO:0016323), synapse (GO:0045202), extracellular exosome (GO:0070062), MPP7-DLG1-LIN7 complex (GO:0097025), presynapse (GO:0098793), postsynaptic density membrane (GO:0098839), 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
transport	2
cell junction	2
cellular anatomical structure	2
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
ear development	1
anatomical structure development	1
cellular component assembly	1
protein-containing complex organization	1
protein binding	1
molecular adaptor activity	1
protein domain specific binding	1
binding	1
membrane	1
cell periphery	1
anchoring junction	1
apical junction complex	1
tight junction	1
basal plasma membrane	1
plasma membrane region	1
extracellular vesicle	1
adherens junction	1
plasma membrane protein complex	1
synapse	1
postsynaptic density	1

Protein interactions and networks

STRING

992 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LIN7A	CASK	O14936	999
LIN7A	PALS1	Q8N3R9	997
LIN7A	APBA1	Q02410	981
LIN7A	PALS2	Q9NZW5	965
LIN7A	PATJ	Q8NI35	962
LIN7A	MPP7	Q5T2T1	878
LIN7A	KIF17	Q9P2E2	846
LIN7A	GRIN2B	Q13224	833
LIN7A	MPP3	Q13368	789
LIN7A	MPP2	Q14168	788
LIN7A	CTNNB1	P35222	780
LIN7A	RTKN	Q9BST9	692
LIN7A	MPP1	Q00013	663
LIN7A	TBR1	Q16650	660
LIN7A	STYK1	Q6J9G0	650

IntAct

496 interactions, top by confidence:

A	B	Type	Score
LIN7A	PALS1	psi-mi:“MI:0915”(physical association)	0.870
PALS1	LIN7A	psi-mi:“MI:0915”(physical association)	0.870
PALS1	LIN7A	psi-mi:“MI:0914”(association)	0.870
LIN7A	CASK	psi-mi:“MI:0915”(physical association)	0.830
CASK	LIN7A	psi-mi:“MI:0915”(physical association)	0.830
MPP2	LIN7A	psi-mi:“MI:0915”(physical association)	0.670
LIN7A	MPP2	psi-mi:“MI:0915”(physical association)	0.670
LIN7A	MPP7	psi-mi:“MI:0915”(physical association)	0.670
LIN7A	PALS2	psi-mi:“MI:0915”(physical association)	0.670
KCNJ2	KCNJ18	psi-mi:“MI:2364”(proximity)	0.660
MPP2	LIN7A	psi-mi:“MI:0914”(association)	0.640
CDA	LIN7A	psi-mi:“MI:0914”(association)	0.640
SLC20A1	LIN7A	psi-mi:“MI:0914”(association)	0.640
ADRA1D	LIN7A	psi-mi:“MI:0914”(association)	0.590
MPDZ	SMCHD1	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
LIN7A	GUCY1A2	psi-mi:“MI:0407”(direct interaction)	0.590
DLGAP4	LIN7A	psi-mi:“MI:0407”(direct interaction)	0.590
CFTR	LIN7A	psi-mi:“MI:0407”(direct interaction)	0.570
	LIN7A	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (90): LIN7A (Two-hybrid), LIN7A (Two-hybrid), LIN7A (Two-hybrid), LIN7A (Two-hybrid), LIN7A (Two-hybrid), MPP5 (Two-hybrid), FAM9B (Two-hybrid), NOTCH2NL (Two-hybrid), LIN7A (Affinity Capture-MS), CADM1 (Affinity Capture-MS), CASK (Affinity Capture-MS), DLG1 (Affinity Capture-MS), EPB41L2 (Affinity Capture-MS), GUCY1A2 (Affinity Capture-MS), GUCY1B3 (Affinity Capture-MS)

ESM2 similar proteins: A1Z7A6, A8WRV1, B4GXC2, B4IT27, B5DK35, E7FDW2, F1M5N7, G5E8P1, G5EEW9, H2KZW3, O14910, O15075, O43150, O75037, O88951, O88952, P41048, P49809, Q01577, Q09284, Q0P5F3, Q24145, Q2KIB6, Q32LM6, Q4IEV4, Q4P3S3, Q5F425, Q5RAA5, Q6NRL1, Q792I0, Q7JVP4, Q7QBW0, Q810W9, Q86BA1, Q8BXK8, Q8JZS0, Q8VHH5, Q93654, Q95QC4, Q95RG8

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

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 138 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
Dopamine Neurotransmitter Release Cycle	5	25.9×	1e-04
Neurexins and neuroligins	9	18.5×	6e-07
Assembly and cell surface presentation of NMDA receptors	6	15.9×	1e-04
RHOQ GTPase cycle	7	13.2×	9e-05
RHO GTPase cycle	13	8.1×	2e-06
CDC42 GTPase cycle	8	6.0×	3e-03
Signaling by Rho GTPases	16	5.7×	3e-06
Signaling by Rho GTPases, Miro GTPases and RHOBTB3	16	5.6×	3e-06

GO biological processes:

GO term	Partners	Fold	FDR
positive regulation of excitatory postsynaptic potential	5	19.8×	2e-03
transport across blood-brain barrier	7	9.4×	3e-03
protein-containing complex assembly	9	7.7×	2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	1
Uncertain significance	28
Likely benign	1
Benign	2

Top pathogenic / likely-pathogenic (3)

Variant ID	HGVS	Classification
57587	GRCh38/hg38 12q21.31(chr12:80393097-81021534)x1	Pathogenic
57589	GRCh38/hg38 12q21.31(chr12:80538484-80798086)x1	Pathogenic
524172	t(12;14)(q14;q13)dn	Likely pathogenic

SpliceAI

1349 predictions. Top by Δscore:

Variant	Effect	Δscore
12:80811680:CACT:C	acceptor_gain	1.0000
12:80811682:CT:C	acceptor_gain	1.0000
12:80811684:C:CC	acceptor_gain	1.0000
12:80845729:CCA:C	donor_gain	1.0000
12:80845729:CCACT:C	donor_gain	1.0000
12:80845838:T:A	donor_gain	1.0000
12:80845936:TTGC:T	acceptor_gain	1.0000
12:80845937:TGCC:T	acceptor_loss	1.0000
12:80845938:GCC:G	acceptor_loss	1.0000
12:80889275:A:AC	donor_gain	1.0000
12:80889276:C:CC	donor_gain	1.0000
12:80889276:CT:C	donor_gain	1.0000
12:80811682:CTCT:C	acceptor_loss	0.9900
12:80811683:TCTG:T	acceptor_loss	0.9900
12:80811684:C:A	acceptor_loss	0.9900
12:80811684:C:G	acceptor_gain	0.9900
12:80811685:T:C	acceptor_loss	0.9900
12:80845723:AACAT:A	donor_loss	0.9900
12:80845724:ACATA:A	donor_loss	0.9900
12:80845726:ATACC:A	donor_loss	0.9900
12:80845727:T:TG	donor_loss	0.9900
12:80845728:A:AC	donor_gain	0.9900
12:80845728:A:AT	donor_loss	0.9900
12:80845729:C:CC	donor_gain	0.9900
12:80845935:GTTGC:G	acceptor_gain	0.9900
12:80845937:TGC:T	acceptor_gain	0.9900
12:80845938:GC:G	acceptor_gain	0.9900
12:80845939:CC:C	acceptor_gain	0.9900
12:80845940:C:CC	acceptor_gain	0.9900
12:80847259:T:A	donor_gain	0.9900

AlphaMissense

1500 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:80811567:A:C	F200L	1.000
12:80811567:A:T	F200L	1.000
12:80811569:A:G	F200L	1.000
12:80811607:C:G	R187P	1.000
12:80811610:A:T	V186E	1.000
12:80811616:A:C	L184R	1.000
12:80811616:A:G	L184P	1.000
12:80811616:A:T	L184Q	1.000
12:80811622:A:T	V182D	1.000
12:80811639:C:A	K176N	1.000
12:80811639:C:G	K176N	1.000
12:80811643:A:C	L175R	1.000
12:80811643:A:G	L175P	1.000
12:80811643:A:T	L175H	1.000
12:80811646:A:G	L174P	1.000
12:80811655:G:T	A171D	1.000
12:80811663:A:C	H168Q	1.000
12:80811663:A:T	H168Q	1.000
12:80811664:T:C	H168R	1.000
12:80811665:G:C	H168D	1.000
12:80811665:G:T	H168N	1.000
12:80811679:A:T	V163E	1.000
12:80845736:G:C	N159K	1.000
12:80845736:G:T	N159K	1.000
12:80845737:T:A	N159I	1.000
12:80845740:A:T	V158E	1.000
12:80845744:A:G	S157P	1.000
12:80845746:A:G	L156P	1.000
12:80845749:A:C	L155R	1.000
12:80845749:A:G	L155P	1.000

dbSNP variants (sampled 300 via entrez): RS1000010803 (12:80912217 A>G), RS1000023867 (12:80883678 C>A,T), RS1000029819 (12:80920615 T>C), RS1000070022 (12:80865493 T>C), RS1000130868 (12:80898557 G>A), RS1000131001 (12:80797133 C>T), RS1000149763 (12:80821736 G>A), RS1000162041 (12:80797456 A>G), RS1000168910 (12:80814535 G>A), RS1000179531 (12:80841396 G>A,C,T), RS1000240069 (12:80918272 C>T), RS1000275703 (12:80804707 T>A,G), RS1000317297 (12:80869401 G>A), RS1000321486 (12:80857451 C>A,T), RS1000329692 (12:80938597 T>C)

Disease associations

OMIM: gene MIM:603380 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST001786_30	Dental caries	9.000000e-06
GCST002618_2	Age-related cataracts (age at onset)	6.000000e-07

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004847	age at onset

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
rs2682818	LIN7A, MIR618		0.00	0

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases expression, increases expression, increases methylation	3
Valproic Acid	affects expression, decreases expression	3
trichostatin A	decreases expression	2
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, affects cotreatment, decreases expression	2
Estradiol	affects cotreatment, increases expression, decreases expression	2
Tetrachlorodibenzodioxin	affects cotreatment, increases expression, decreases expression	2
Aflatoxin B1	decreases expression, decreases methylation	2
aristolochic acid I	decreases expression	1
FR900359	increases phosphorylation	1
geldanamycin	increases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	increases methylation	1
sodium arsenite	increases expression	1
di-n-butylphosphoric acid	affects expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Sunitinib	increases expression	1
Vorinostat	increases expression	1
Leflunomide	increases expression	1
Acetaminophen	decreases expression	1
Amiodarone	increases expression	1
Calcitriol	decreases expression, affects cotreatment	1
Coumestrol	affects cotreatment, decreases expression	1
Demecolcine	decreases expression	1
Diethylhexyl Phthalate	decreases expression	1
Doxorubicin	decreases expression	1
Formaldehyde	decreases expression	1

Clinical trials (associated diseases)

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