MIA2

Summary

MIA2 (MIA SH3 domain ER export factor 2, HGNC:18432) is a protein-coding gene on chromosome 14q13.2, encoding Melanoma inhibitory activity protein 2 (Q96PC5). Plays a role in the transport of cargos that are too large to fit into COPII-coated vesicles and require specific mechanisms to be incorporated into membrane-bound carriers and exported from the endoplasmic reticulum.

This gene encodes s receptor in the endoplasmic reticulum, which plays a role in the export of large pre-chylomicrons and pre-very low density lipoproteins (pre-VLDLs). Three major classes of transcripts are generated from this gene- melanoma inhibitory activity 2-specific transcripts, cTAGE family member 5-specific transcripts and transcripts that include exons from both these transcript species (TANGO1-like or TALI). Additionally, alternative splicing in these transcripts results in multiple transcript variants encoding multiple isoforms.

Source: NCBI Gene 4253 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 290 total
• MANE Select transcript: NM_001329214

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18432
Approved symbol	MIA2
Name	MIA SH3 domain ER export factor 2
Location	14q13.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ22404, TALI, MEA6, cTAGE-5A, cTAGE-5B, cTAGE-5C, cTAGE-5D, MGEA11
Ensembl gene	ENSG00000150527
Ensembl biotype	protein_coding
OMIM	602132
Entrez	4253

Gene structure

Transcript identifiers

Ensembl transcripts: 24 — 20 protein_coding, 2 retained_intron, 2 protein_coding_CDS_not_defined

ENST00000280082, ENST00000280083, ENST00000341502, ENST00000341749, ENST00000348007, ENST00000396158, ENST00000396165, ENST00000553352, ENST00000553383, ENST00000553728, ENST00000554392, ENST00000555143, ENST00000555716, ENST00000556148, ENST00000556593, ENST00000556990, ENST00000557038, ENST00000557148, ENST00000640607, ENST00000869684, ENST00000869685, ENST00000869686, ENST00000869687, ENST00000869688

RefSeq mRNA: 30 — MANE Select: NM_001329214 NM_001247988, NM_001247989, NM_001247990, NM_001329214, NM_001354137, NM_001354138, NM_001354139, NM_001354140, NM_001354141, NM_001354142, NM_001354143, NM_001354144, NM_001354145, NM_001354146, NM_001354147, NM_001354148, NM_001354149, NM_001354150, NM_001354151, NM_001354152, NM_001354153, NM_001354154, NM_001354155, NM_001354156, NM_001354157, NM_005930, NM_054024, NM_203354, NM_203355, NM_203356

CCDS: CCDS58316, CCDS58317, CCDS86384, CCDS86385, CCDS86386, CCDS9672, CCDS9673, CCDS9674, CCDS9675, CCDS9676

Canonical transcript exons

ENST00000640607 — 29 exons

Exon	Start	End
ENSE00002505506	39253071	39253171
ENSE00003803117	39350098	39350694
ENSE00003805542	39233915	39234229
ENSE00003811564	39347713	39347771
ENSE00003811579	39293271	39293381
ENSE00003811666	39303478	39303524
ENSE00003811763	39304291	39304381
ENSE00003811819	39252748	39252966
ENSE00003811878	39313340	39313441
ENSE00003811919	39279337	39279358
ENSE00003811939	39317944	39318011
ENSE00003812003	39320928	39321056
ENSE00003812064	39314739	39314799
ENSE00003812133	39302129	39302249
ENSE00003812232	39236922	39237055
ENSE00003812244	39291019	39291096
ENSE00003812712	39294000	39294071
ENSE00003812744	39348743	39348977
ENSE00003812941	39326864	39327022
ENSE00003813287	39276934	39277065
ENSE00003813307	39294925	39295029
ENSE00003813407	39319209	39319291
ENSE00003813670	39345904	39346026
ENSE00003813708	39246911	39248141
ENSE00003813803	39279449	39279537
ENSE00003813830	39299864	39299986
ENSE00003813975	39308449	39308587
ENSE00003814063	39315683	39315718
ENSE00003814190	39240561	39240647

Expression profiles

Bgee: expression breadth ubiquitous, 279 present calls, max score 97.11.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 20.8234 / max 265.9175, expressed in 1795 samples.

FANTOM5 promoters (15 alternative TSS)

Promoter ID	TPM avg	Samples expressed
139375	8.4536	1714
139365	3.0614	928
139374	2.9499	1334
139373	2.7068	1337
139371	1.0695	419
139372	0.8545	427
139363	0.4653	75
139366	0.2229	106
139369	0.2064	84
139370	0.2030	64

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right lobe of liver	UBERON:0001114	97.11	gold quality
mucosa of transverse colon	UBERON:0004991	94.39	gold quality
islet of Langerhans	UBERON:0000006	94.38	gold quality
body of pancreas	UBERON:0001150	94.06	gold quality
pancreas	UBERON:0001264	93.43	gold quality
rectum	UBERON:0001052	93.38	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	93.08	gold quality
jejunal mucosa	UBERON:0000399	93.02	gold quality
colonic epithelium	UBERON:0000397	93.01	gold quality
gall bladder	UBERON:0002110	92.80	gold quality
liver	UBERON:0002107	92.63	gold quality
mucosa of paranasal sinus	UBERON:0005030	92.60	gold quality
calcaneal tendon	UBERON:0003701	92.39	gold quality
adrenal tissue	UBERON:0018303	92.32	gold quality
small intestine Peyer’s patch	UBERON:0003454	91.91	gold quality
minor salivary gland	UBERON:0001830	91.88	gold quality
small intestine	UBERON:0002108	91.81	gold quality
sperm	CL:0000019	91.67	gold quality
right adrenal gland cortex	UBERON:0035827	91.65	gold quality
saliva-secreting gland	UBERON:0001044	91.43	gold quality
lower esophagus mucosa	UBERON:0035834	91.20	gold quality
right adrenal gland	UBERON:0001233	91.08	gold quality
duodenum	UBERON:0002114	90.97	gold quality
esophagus mucosa	UBERON:0002469	90.88	gold quality
adult mammalian kidney	UBERON:0000082	90.76	gold quality
left adrenal gland	UBERON:0001234	90.69	gold quality
body of stomach	UBERON:0001161	90.68	gold quality
hindlimb stylopod muscle	UBERON:0004252	90.52	gold quality
left adrenal gland cortex	UBERON:0035825	90.49	gold quality
granulocyte	CL:0000094	90.44	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-10287	yes	44.66
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

20 targeting MIA2, 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-4262	100.00	73.26	3931
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-190A-3P	100.00	80.35	5520
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
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-4307	99.82	70.45	3374
HSA-MIR-200A-5P	99.76	69.10	949
HSA-MIR-200B-5P	99.76	69.05	948
HSA-MIR-33A-3P	99.70	70.27	3362
HSA-MIR-5093	99.67	69.26	2291
HSA-MIR-543	99.52	69.03	2595
HSA-MIR-5584-5P	99.49	68.22	2814
HSA-MIR-4311	99.31	70.47	3041
HSA-MIR-3978	99.24	68.39	2201
HSA-MIR-4426	99.17	66.74	1949
HSA-MIR-600	97.07	66.73	1259
HSA-MIR-552-3P	96.68	64.12	1026

Literature-anchored findings (GeneRIF, showing 12)

• Data indicate that MIA2 represents a potential novel acute phase protein and MIA2 expression responds to liver damage in chronic liver diseases. (PMID:12586826)
• The novel gene MIA2 acts as a tumour suppressor in hepatocellular carcinoma. (PMID:17881540)
• population and bioinformatic analysis of MGEA6 P521A variation as a risk factor for Fahr’s disease; genetic screen data show this mutation is very rare; bioinformatics analysis provided conflicting findings (PMID:20838928)
• cTAGE5 forms a complex with TANGO1 (MIA3), a previously characterized cargo receptor for collagen VII (PMID:21525241)
• HBx activates hepatoma cell growth and proliferation through repression of the potential tumor suppressor MIA2. (PMID:22120627)
• 22 members of an Iranian family with basal ganglia calfication as well as 100 controls were genotyped for the C>G P521A variant of CTAGE5, but none were found. (PMID:23054591)
• Findings suggest that the roles of MIA2 might be based on the variety of the integrins and the subtypes of mitogen-activated protein kinase in oral carcinoma. (PMID:23511560)
• Sec12 recruitment to endoplasmic reticulum exit sites is organized by its direct interaction with cTAGE5, a previously characterized collagen cargo receptor component, which functions together with TANGO1 at endoplasmic reticulum exit sites. (PMID:25202031)
• These findings define an interaction between the common MIA2(I141M) variant and the ER stress/UPR system and specify a subgroup of PDAC patients who are more likely to benefit from adjuvant chemotherapy. (PMID:25657029)
• In this study, we identified specific and critical residues in the Sec12-binding region of cTAGE5 (E75A K76A, K89A, and S97A) and confirmed that cTAGE5-mediated Sec12 accumulation at ER exit sites is required for collagen VII secretion. (PMID:27170179)
• TANGO1/CTAGE5 receptor serves as a polyvalent template for assembly of large COPII coats. (PMID:27551091)
• These data showed that the NRZ tether is required for TANGO1 to assemble into a ring and indicated that stable complexes of TANGO1, cTAGE5 and TANGO1-short, recruit the tether. (PMID:29513218)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	Mia2	ENSMUSG00000021000
rattus_norvegicus	Mia2	ENSRNOG00000005101
drosophila_melanogaster	Tango1	FBGN0286898

Paralogs (10): OTOR (ENSG00000125879), MIA3 (ENSG00000154305), SPZ1 (ENSG00000164299), CTAGE1 (ENSG00000212710), CTAGE9 (ENSG00000236761), MIA (ENSG00000261857), CTAGE15 (ENSG00000271079), CTAGE6 (ENSG00000271321), CTAGE4 (ENSG00000288784), CTAGE8 (ENSG00000289604)

Protein

Protein identifiers

Melanoma inhibitory activity protein 2 — Q96PC5 (reviewed: Q96PC5)

Alternative names: CTAGE family member 5 ER export factor, Cutaneous T-cell lymphoma-associated antigen 5, Meningioma-expressed antigen 6/11

All UniProt accessions (5): Q96PC5, G3V3C4, G3V4M1, G3V599, G3V5K6

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in the transport of cargos that are too large to fit into COPII-coated vesicles and require specific mechanisms to be incorporated into membrane-bound carriers and exported from the endoplasmic reticulum. Plays a role in the secretion of lipoproteins, pre-chylomicrons and pre-VLDLs, by participating in their export from the endoplasmic reticulum. Thereby, may play a role in cholesterol and triglyceride homeostasis. Required for collagen VII (COL7A1) secretion by loading COL7A1 into transport carriers and recruiting PREB/SEC12 at the endoplasmic reticulum exit sites.

Subunit / interactions. Interacts with MIA3. Interacts with the COPII coat subunits SEC23A, SEC23B and maybe SEC24C. Interacts with PREB; recruits PREB to endoplasmic reticulum exit sites. Interacts with APOB.

Subcellular location. Endoplasmic reticulum membrane.

Tissue specificity. Highly expressed in liver and weakly in testis. Expression was higher in patients with severe fibrosis or inflammation and chronic hepatitis. Isoform 1 is specifically expressed in lung, testis, small intestine, colon, pancreas, kidney, liver and prostate. Isoform 8 is expressed only in testis (at the protein level). Isoform 8 (at protein level) and isoform 9 are expressed in cutaneous T-cell lymphoma (CTCL) cell lines, colorectal carcinomas, breast carcinomas and melanoma. Isoform 9, but not isoform 5A, is expressed in head and neck squamous cell carcinoma.

Disease relevance. Autoantibodies against MIA2 are present in several cancer types, including benign meningioma and cutaneous T-cell lymphoma (CTCL).

Domain organisation. The proline-rich domain (PRD) contains repeated PPP motifs. A single PPP motif is necessary and sufficient to mediate interaction with the COPII coat subunits SEC23A and SEC23B. The coiled coil domains mediate interaction with MIA3. The first coiled coil domain mediates interaction with PREB.

Miscellaneous. Readthrough transcript producing a functional fusion protein MIA2-CTAGE5 with similarity to MIA3.

Similarity. Belongs to the MIA/OTOR family.

Isoforms (12)

UniProt ID	Names	Canonical?
Q96PC5-3	1, TALI	yes
Q96PC5-2	2
Q96PC5-5	4
Q96PC5-6	5
Q96PC5-7	6, MEA6
Q96PC5-8	7, MEA11
Q96PC5-9	8, 5A
Q96PC5-10	9, 5B
Q96PC5-11	10
Q96PC5-12	11
Q96PC5-13	12
Q96PC5-14	13

RefSeq proteins (30): NP_001234917, NP_001234918, NP_001234919, NP_001316143, NP_001341066, NP_001341067, NP_001341068, NP_001341069, NP_001341070, NP_001341071, NP_001341072, NP_001341073, NP_001341074, NP_001341075, NP_001341076, NP_001341077, NP_001341078, NP_001341079, NP_001341080, NP_001341081, NP_001341082, NP_001341083, NP_001341084, NP_001341085, NP_001341086, NP_005921, NP_473365, NP_976229, NP_976230, NP_976231 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001452	SH3_domain	Domain
IPR035555	MIA2_SH3	Domain
IPR036028	SH3-like_dom_sf	Homologous_superfamily
IPR051500	cTAGE_MIA/OTOR	Family

Pfam: PF07653

UniProt features (67 total): splice variant 15, sequence variant 12, sequence conflict 10, region of interest 7, compositionally biased region 7, mutagenesis site 4, topological domain 3, coiled-coil region 2, glycosylation site 2, signal peptide 1, chain 1, intramembrane region 1, transmembrane region 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96PC5-F1	54.91	0.18

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): 59, 368

Mutagenesis-validated functional residues (4):

Position	Phenotype
679	no effect on interaction with perb.
697	loss of interaction with perb. unable to recruit perb to the endoplasmic reticulum exit sites. loss of function in colla
705	decreased interaction with perb. no effect on interaction with mia3.
720	no effect on interaction with perb.

Function

Pathways and Gene Ontology

Reactome pathways

8 pathways

ID	Pathway
R-HSA-5694530	Cargo concentration in the ER
R-HSA-199977	ER to Golgi Anterograde Transport
R-HSA-199991	Membrane Trafficking
R-HSA-392499	Metabolism of proteins
R-HSA-446203	Asparagine N-linked glycosylation
R-HSA-5653656	Vesicle-mediated transport
R-HSA-597592	Post-translational protein modification
R-HSA-948021	Transport to the Golgi and subsequent modification

MSigDB gene sets: 247 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_UP, TAATAAT_MIR126, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, CHUANG_OXIDATIVE_STRESS_RESPONSE_UP, MORF_ATRX, GOBP_VESICLE_MEDIATED_TRANSPORT, HNF1_Q6, REACTOME_MEMBRANE_TRAFFICKING, GOBP_PROTEIN_LOCALIZATION_TO_ENDOPLASMIC_RETICULUM, GOBP_ENDOPLASMIC_RETICULUM_TO_GOLGI_VESICLE_MEDIATED_TRANSPORT, MYCMAX_01, DACOSTA_UV_RESPONSE_VIA_ERCC3_TTD_DN, SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_DN, GOBP_SECRETION, IRF_Q6

GO Biological Process (6): endoplasmic reticulum to Golgi vesicle-mediated transport (GO:0006888), protein secretion (GO:0009306), protein exit from endoplasmic reticulum (GO:0032527), vesicle cargo loading (GO:0035459), lipoprotein transport (GO:0042953), protein localization to endoplasmic reticulum exit site (GO:0070973)

GO Molecular Function (3): enzyme activator activity (GO:0008047), cargo receptor activity (GO:0038024), protein binding (GO:0005515)

GO Cellular Component (4): endoplasmic reticulum (GO:0005783), endoplasmic reticulum membrane (GO:0005789), membrane (GO:0016020), endoplasmic reticulum exit site (GO:0070971)

Reactome top-level categories

Rollup of top-7 pathways:

Category	Pathways
ER to Golgi Anterograde Transport	1
Membrane Trafficking	1
Transport to the Golgi and subsequent modification	1
Vesicle-mediated transport	1
Post-translational protein modification	1
Metabolism of proteins	1
Asparagine N-linked glycosylation	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	3
protein transport	2
vesicle-mediated transport	2
cellular anatomical structure	2
intercellular transport	1
intracellular transport	1
Golgi vesicle transport	1
secretion by cell	1
establishment of protein localization to extracellular region	1
protein localization to extracellular region	1
intracellular protein transport	1
transport	1
lipoprotein localization	1
protein localization to endoplasmic reticulum	1
catalytic activity	1
enzyme regulator activity	1
molecular function activator activity	1
molecular_function	1
molecular adaptor activity	1
binding	1
endomembrane system	1
intracellular membrane-bounded organelle	1
organelle membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1
endoplasmic reticulum	1

Protein interactions and networks

STRING

1023 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MIA2	PREB	Q9HCU5	985
MIA2	CCDC68	Q9H2F9	960
MIA2	MIA3	Q5JRA6	947
MIA2	SEC16A	O15027	842
MIA2	SEC24B	O95487	781
MIA2	SEC13	P55735	704
MIA2	LMAN1	P49257	700
MIA2	TRAPPC2	P0DI81	657
MIA2	KLHL12	Q53G59	613
MIA2	SEC31A	O94979	584
MIA2	SEC24D	O94855	574
MIA2	SAR1B	Q9Y6B6	562
MIA2	SHISA4	Q96DD7	551
MIA2	SAR1A	Q9NR31	544
MIA2	SURF4	O15260	537

IntAct

98 interactions, top by confidence:

A	B	Type	Score
QPRT	PIK3C2A	psi-mi:“MI:0914”(association)	0.640
MIA2	RGPD8	psi-mi:“MI:0914”(association)	0.640
STX12	SNAP23	psi-mi:“MI:0914”(association)	0.640
NIPAL1	ESYT2	psi-mi:“MI:0914”(association)	0.640
SLC39A5	FAM171A2	psi-mi:“MI:0914”(association)	0.640
MIA2	PSMA3	psi-mi:“MI:0915”(physical association)	0.560
MIA2	TTC23L	psi-mi:“MI:0915”(physical association)	0.560
MIA2	MAGEB18	psi-mi:“MI:0915”(physical association)	0.560
EMILIN1	MIA2	psi-mi:“MI:0915”(physical association)	0.560
MIA2	SS18L1	psi-mi:“MI:0915”(physical association)	0.560
TLE5	MIA2	psi-mi:“MI:0915”(physical association)	0.560
MIA2	CEP57	psi-mi:“MI:0915”(physical association)	0.560
MIA2	CCHCR1	psi-mi:“MI:0915”(physical association)	0.560
MIA2	RASAL2	psi-mi:“MI:0915”(physical association)	0.560
MAGEB18	MIA2	psi-mi:“MI:0915”(physical association)	0.560
MIA2	EMILIN1	psi-mi:“MI:0915”(physical association)	0.560
CEP57	MIA2	psi-mi:“MI:0915”(physical association)	0.560
CCHCR1	MIA2	psi-mi:“MI:0915”(physical association)	0.560
SS18L1	MIA2	psi-mi:“MI:0915”(physical association)	0.560
PSMA3	MIA2	psi-mi:“MI:0915”(physical association)	0.560
MIA2	TLE5	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (32): MIA2 (Synthetic Growth Defect), MIA2 (Synthetic Lethality), MIA2 (Proximity Label-MS), MIA2 (Proximity Label-MS), MIA2 (Proximity Label-MS), MIA2 (Proximity Label-MS), MIA2 (Proximity Label-MS), MIA2 (Affinity Capture-MS), MIA2 (Proximity Label-MS), CHSY1 (Affinity Capture-MS), MKRN3 (Affinity Capture-MS), CLIC3 (Affinity Capture-MS), MIA2 (Affinity Capture-MS), MIA2 (Affinity Capture-MS), MIA2 (Proximity Label-MS)

ESM2 similar proteins: A2AM05, A2BDC9, A2VD12, A2VE10, A5D8S1, B1AJZ9, O00461, O75071, P04233, P04441, P07106, P10247, P24054, P70663, Q08D19, Q14515, Q32N32, Q4KLH6, Q4V9H3, Q5BJK8, Q5PQS2, Q5R5X4, Q5R6R3, Q5R8Y4, Q5R9L2, Q5T8D3, Q5TB80, Q5ZHQ6, Q5ZKQ5, Q5ZM60, Q640L3, Q6P2L7, Q6P4E1, Q6Y685, Q6ZQ06, Q70YC5, Q86TE4, Q8BG89, Q8BMK4, Q8BVV7

Diamond homologs: A4D2H0, A4FU28, P0CG41, Q86UF2, Q8IX94, Q8IX95, Q91ZV0, Q96PC5, Q96RT6, P52735, Q0VC16, Q16674, Q28038, Q5JRA6, Q60992, Q61865, Q62946, Q8BI84, Q9I8P5, Q9I8P6, Q9JIE3, Q9NRC9, Q9R0C8, Q9UKW4, Q9VMA7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	225
Likely benign	24
Benign	3

Top pathogenic / likely-pathogenic (0)

SpliceAI

5524 predictions. Top by Δscore:

Variant	Effect	Δscore
14:39236910:T:G	acceptor_gain	1.0000
14:39240556:GACA:G	acceptor_loss	1.0000
14:39240558:CA:C	acceptor_loss	1.0000
14:39240559:A:AC	acceptor_loss	1.0000
14:39240559:A:AG	acceptor_gain	1.0000
14:39240559:A:AT	acceptor_loss	1.0000
14:39240560:G:GA	acceptor_gain	1.0000
14:39240560:G:GC	acceptor_gain	1.0000
14:39240560:G:T	acceptor_loss	1.0000
14:39240560:GA:G	acceptor_gain	1.0000
14:39240560:GAA:G	acceptor_gain	1.0000
14:39240560:GAAA:G	acceptor_gain	1.0000
14:39240643:CGAAA:C	donor_gain	1.0000
14:39240644:GAAA:G	donor_gain	1.0000
14:39240644:GAAAG:G	donor_gain	1.0000
14:39240645:AAA:A	donor_gain	1.0000
14:39240646:AA:A	donor_gain	1.0000
14:39240647:AG:A	donor_loss	1.0000
14:39240648:G:GG	donor_gain	1.0000
14:39240649:T:G	donor_loss	1.0000
14:39240650:GAG:G	donor_loss	1.0000
14:39240651:A:AG	donor_gain	1.0000
14:39240652:G:GG	donor_gain	1.0000
14:39267521:GG:G	donor_gain	1.0000
14:39267522:GG:G	donor_gain	1.0000
14:39276930:GAA:G	acceptor_loss	1.0000
14:39276932:A:T	acceptor_loss	1.0000
14:39276933:GGTT:G	acceptor_gain	1.0000
14:39279448:GGAC:G	acceptor_gain	1.0000
14:39279535:GAG:G	donor_gain	1.0000

AlphaMissense

9349 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
14:39314756:T:C	L1046P	0.996
14:39314746:G:C	A1043P	0.994
14:39308581:T:C	L1004P	0.993
14:39313366:G:C	R1015P	0.993
14:39314744:G:C	R1042P	0.993
14:39237009:T:A	V68D	0.992
14:39236979:T:C	L58P	0.991
14:39240583:T:C	F91S	0.991
14:39313416:G:C	A1032P	0.991
14:39237044:T:A	W80R	0.990
14:39237044:T:C	W80R	0.990
14:39294925:G:C	A798P	0.990
14:39313345:T:C	L1008S	0.990
14:39313387:T:C	L1022P	0.989
14:39313429:T:C	L1036P	0.989
14:39237051:G:A	G82E	0.987
14:39240577:G:A	G89E	0.987
14:39240583:T:G	F91C	0.987
14:39321022:A:C	R1154S	0.987
14:39321022:A:T	R1154S	0.987
14:39237046:G:C	W80C	0.986
14:39237046:G:T	W80C	0.986
14:39237047:G:C	A81P	0.986
14:39240582:T:C	F91L	0.985
14:39240584:T:A	F91L	0.985
14:39240584:T:G	F91L	0.985
14:39314785:T:C	S1056P	0.985
14:39314788:T:G	Y1057D	0.985
14:39321021:G:C	R1154T	0.984
14:39236985:T:C	F60S	0.983

dbSNP variants (sampled 300 via entrez): RS1000015523 (14:39365138 T>C), RS1000026155 (14:39369085 T>A,G), RS1000031725 (14:39243721 C>A), RS1000046190 (14:39294652 G>A), RS1000078052 (14:39317450 G>A), RS1000095651 (14:39331283 C>CT,CTTT), RS1000126599 (14:39325777 G>A,T), RS1000157763 (14:39325994 A>G), RS1000162873 (14:39288922 GTTTA>G,GTTTATTTA), RS1000174275 (14:39359673 C>G), RS1000184633 (14:39269727 C>G), RS1000229677 (14:39354637 T>C,G), RS1000240093 (14:39263202 T>A), RS1000247199 (14:39279118 G>A), RS1000264531 (14:39320468 T>G)

Disease associations

OMIM: gene MIM:602132 | 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
GCST009391_1761	Metabolite levels	4.000000e-06
GCST90002401_71	Platelet distribution width	8.000000e-09

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0010370	lysophosphatidylethanolamine 20:4 measurement
EFO:0007984	platelet component distribution width

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases expression	5
Cyclosporine	decreases expression, increases expression, affects expression	3
Aflatoxin B1	affects expression, decreases expression, decreases methylation	3
bisphenol A	affects expression, affects cotreatment, decreases expression	2
Air Pollutants	decreases expression, increases abundance, increases expression	2
Tetrachlorodibenzodioxin	increases expression	2
aristolochic acid I	decreases expression	1
dicrotophos	decreases expression	1
urushiol	increases expression	1
triphenyl phosphate	affects expression	1
glycidyl methacrylate	decreases expression	1
trichostatin A	increases expression	1
beta-lapachone	decreases expression, increases expression	1
sulforaphane	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression, increases expression	1
cobaltous chloride	increases expression	1
butyraldehyde	decreases expression	1
coumarin	decreases phosphorylation	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	increases expression	1
CGP 52608	affects binding, increases reaction	1
K 7174	increases expression	1
Grape Seed Proanthocyanidins	affects cotreatment, decreases expression	1
NSC 689534	increases expression, affects binding	1
bisphenol AF	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Leflunomide	increases expression	1
Acetaminophen	decreases expression	1
Air Pollutants, Occupational	affects expression, increases abundance, increases expression	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_C6Y3	HAP1 CTAGE5 (-) 1	Cancer cell line	Male

Clinical trials (associated diseases)

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