GTF2A2

Summary

GTF2A2 (general transcription factor IIA subunit 2, HGNC:4647) is a protein-coding gene on chromosome 15q22.2, encoding Transcription initiation factor IIA subunit 2 (P52657). TFIIA is a component of the transcription machinery of RNA polymerase II and plays an important role in transcriptional activation. It is a common-essential gene (DepMap: required in 99.3% of cancer cell lines).

Accurate transcription initiation on TATA-containing class II genes involves the ordered assembly of RNA polymerase II (POLR2A; MIM 180660) and the general initiation factors TFIIA, TFIIB (MIM 189963), TFIID (MIM 313650), TFIIE (MIM 189962), TFIIF (MIM 189968), TFIIG/TFIIJ, and TFIIH (MIM 189972). The first step involves recognition of the TATA element by the TATA-binding subunit (TBP; MIM 600075) and may be regulated by TFIIA, a factor that interacts with both TBP and a TBP-associated factor (TAF; MIM 600475) in TFIID. TFIIA has 2 subunits (43 and 12 kD) in yeast and 3 subunits in higher eukaryotes. In HeLa extracts, it consists of a 35-kD alpha subunit and a 19-kD beta subunit encoded by the N- and C-terminal regions of GTF2A1 (MIM 600520), respectively, and a 12-kD gamma subunit encoded by GTF2A2 (DeJong et al., 1995 [PubMed 7724559]).

Source: NCBI Gene 2958 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 21 total
• Cancer dependency (DepMap): dependent in 99.3% of screened cell lines (common-essential)
• MANE Select transcript: NM_004492

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:4647
Approved symbol	GTF2A2
Name	general transcription factor IIA subunit 2
Location	15q22.2
Locus type	gene with protein product
Status	Approved
Aliases	TFIIA, HsT18745
Ensembl gene	ENSG00000140307
Ensembl biotype	protein_coding
OMIM	600519
Entrez	2958

Gene structure

Transcript identifiers

Ensembl transcripts: 25 — 21 protein_coding, 3 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000267869, ENST00000396060, ENST00000396061, ENST00000396063, ENST00000396064, ENST00000472508, ENST00000480768, ENST00000484743, ENST00000559141, ENST00000559706, ENST00000885929, ENST00000885930, ENST00000885931, ENST00000885932, ENST00000885933, ENST00000885934, ENST00000885935, ENST00000933396, ENST00000933397, ENST00000933398, ENST00000933399, ENST00000933400, ENST00000933401, ENST00000933402, ENST00000941618

RefSeq mRNA: 3 — MANE Select: NM_004492 NM_001320929, NM_001320930, NM_004492

CCDS: CCDS10173

Canonical transcript exons

ENST00000396060 — 5 exons

Exon	Start	End
ENSE00000942369	59650669	59650773
ENSE00001141539	59652206	59652326
ENSE00001523738	59657406	59657515
ENSE00001685599	59638062	59639157
ENSE00003467309	59642136	59642262

Expression profiles

Bgee: expression breadth ubiquitous, 297 present calls, max score 99.42.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 97.3874 / max 845.8431, expressed in 1826 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
150284	87.7867	1825
150283	9.4431	1735
150282	0.1242	28
150281	0.0334	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	99.42	gold quality
right testis	UBERON:0004534	99.37	gold quality
adult organism	UBERON:0007023	98.82	gold quality
testis	UBERON:0000473	98.59	gold quality
ventricular zone	UBERON:0003053	98.23	gold quality
male germ cell	CL:0000015	98.22	gold quality
sperm	CL:0000019	98.11	gold quality
ganglionic eminence	UBERON:0004023	97.95	gold quality
parotid gland	UBERON:0001831	97.81	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	97.44	gold quality
heart right ventricle	UBERON:0002080	97.33	gold quality
adenohypophysis	UBERON:0002196	97.08	gold quality
monocyte	CL:0000576	97.04	gold quality
cortical plate	UBERON:0005343	96.99	gold quality
mononuclear cell	CL:0000842	96.89	gold quality
leukocyte	CL:0000738	96.86	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	96.85	gold quality
pituitary gland	UBERON:0000007	96.81	gold quality
mucosa of transverse colon	UBERON:0004991	96.80	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	96.79	gold quality
diaphragm	UBERON:0001103	96.77	gold quality
pons	UBERON:0000988	96.73	gold quality
hindlimb stylopod muscle	UBERON:0004252	96.72	gold quality
adrenal tissue	UBERON:0018303	96.71	gold quality
pharyngeal mucosa	UBERON:0000355	96.69	gold quality
vena cava	UBERON:0004087	96.69	gold quality
lower esophagus mucosa	UBERON:0035834	96.68	gold quality
left coronary artery	UBERON:0001626	96.59	gold quality
rectum	UBERON:0001052	96.54	gold quality
spinal cord	UBERON:0002240	96.54	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-134144	yes	30.20
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

54 targeting GTF2A2, 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-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-1236-3P	99.94	68.04	1695
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-3681-3P	99.88	70.46	2254
HSA-MIR-544A	99.84	68.66	1965
HSA-MIR-6515-3P	99.82	68.19	1933
HSA-MIR-6844	99.82	70.69	2423
HSA-MIR-3975	99.62	65.97	697
HSA-MIR-548AV-5P	99.60	70.84	2107
HSA-MIR-548K	99.60	70.84	2107
HSA-MIR-888-3P	99.53	69.77	1057
HSA-MIR-8054	99.48	70.81	2084
HSA-MIR-942-5P	99.41	68.40	1977
HSA-MIR-6839-3P	99.39	68.86	1301
HSA-MIR-103A-1-5P	99.39	67.78	1545
HSA-MIR-103A-2-5P	99.39	67.72	1577
HSA-MIR-4797-5P	99.39	68.01	1354
HSA-MIR-4999-5P	99.35	69.15	926
HSA-MIR-6719-3P	99.29	67.78	1387
HSA-MIR-548V	99.29	69.47	1157
HSA-MIR-3191-5P	99.24	66.52	1722
HSA-MIR-5693	99.24	66.67	1106

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 99.3% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 2)

• transcription factor IIA may regulate the intracellular molecular state and the function of TATA-binding protein-like protein (TLP) through its property of binding to TLP (PMID:14570910)
• Data suggest that many TATA-box-containing promoters contain a TFIIA recognition element (IIARE) that activates transcription by increasing the recruitment of RNA polymerase II, TFIIA (TF2A1/TF2A2 subunits), TAF4, and P300. (TAF4 = TATA box binding protein (TBP)-associated factor, RNA polymerase II, C1; P300 = E1A binding protein p300) (PMID:28539359)

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
danio_rerio	gtf2a2	ENSDARG00000053685
mus_musculus	Gtf2a2	ENSMUSG00000033543
rattus_norvegicus		ENSRNOG00000064241
drosophila_melanogaster	TfIIA-S	FBGN0013347
drosophila_melanogaster	TfIIA-S-2	FBGN0040338
caenorhabditis_elegans		WBGENE00013736
caenorhabditis_elegans		WBGENE00015150

Protein

Protein identifiers

Transcription initiation factor IIA subunit 2 — P52657 (reviewed: P52657)

Alternative names: General transcription factor IIA subunit 2, TFIIA p12 subunit, Transcription initiation factor IIA gamma chain

All UniProt accessions (4): P52657, A0A0B4J1Z5, A8MYR4, H0YK39

UniProt curated annotations — full annotation on UniProt →

Function. TFIIA is a component of the transcription machinery of RNA polymerase II and plays an important role in transcriptional activation. TFIIA in a complex with TBP mediates transcriptional activity.

Subunit / interactions. TFIIA is a heterodimer of the large unprocessed subunit 1 and a small subunit gamma. It was originally believed to be a heterotrimer of an alpha (p35), a beta (p19) and a gamma subunit (p12). Interacts with NCOA6 general coactivator. TFIIA forms a complex with TBP. Interacts with HSF1 (via transactivation domain). Part of TBP-based Pol II pre-initiation complex (PIC), in which Pol II core assembles with general transcription factors and other specific initiation factors including GTF2E1, GTF2E2, GTF2F1, GTF2F2, TCEA1, ERCC2, ERCC3, GTF2H2, GTF2H3, GTF2H4, GTF2H5, GTF2A1, GTF2A2, GTF2B and TBP; this large multi-subunit PIC complex mediates DNA unwinding and targets Pol II core to the transcription start site where the first phosphodiester bond forms. (Microbial infection) Interacts with SV40 Large T antigen.

Subcellular location. Nucleus.

Similarity. Belongs to the TFIIA subunit 2 family.

RefSeq proteins (3): NP_001307858, NP_001307859, NP_004483* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003194	TFIIA_gsu	Family
IPR009083	TFIIA_a-hlx	Homologous_superfamily
IPR009088	TFIIA_b-brl	Homologous_superfamily
IPR015871	TFIIA_gsu_C	Domain
IPR015872	TFIIA_gsu_N	Domain

Pfam: PF02268, PF02751

UniProt features (7 total): helix 3, strand 3, chain 1

Structure

Experimental structures (PDB)

54 structures, top 30 by resolution.

PDB	Method	Resolution (Å)
1NVP	X-RAY DIFFRACTION	2.1
5M4S	X-RAY DIFFRACTION	2.38
7NVU	ELECTRON MICROSCOPY	2.5
7NVS	ELECTRON MICROSCOPY	2.8
7NVT	ELECTRON MICROSCOPY	2.9
8S52	ELECTRON MICROSCOPY	2.9
7ZWD	ELECTRON MICROSCOPY	3
7ZX8	ELECTRON MICROSCOPY	3
8S51	ELECTRON MICROSCOPY	3.1
7ZWC	ELECTRON MICROSCOPY	3.2
7EGB	ELECTRON MICROSCOPY	3.3
7ZX7	ELECTRON MICROSCOPY	3.4
8S5N	ELECTRON MICROSCOPY	3.4
7ZXE	ELECTRON MICROSCOPY	3.5
7EG9	ELECTRON MICROSCOPY	3.7
8BZ1	ELECTRON MICROSCOPY	3.8
5IYB	ELECTRON MICROSCOPY	3.9
5IYC	ELECTRON MICROSCOPY	3.9
5IYD	ELECTRON MICROSCOPY	3.9
7EGC	ELECTRON MICROSCOPY	3.9
8BVW	ELECTRON MICROSCOPY	4
7ENA	ELECTRON MICROSCOPY	4.07
7EGA	ELECTRON MICROSCOPY	4.1
8BYQ	ELECTRON MICROSCOPY	4.1
7ENC	ELECTRON MICROSCOPY	4.13
8GXS	ELECTRON MICROSCOPY	4.16
7EDX	ELECTRON MICROSCOPY	4.5
7NVR	ELECTRON MICROSCOPY	4.5
7LBM	ELECTRON MICROSCOPY	4.8
8GXQ	ELECTRON MICROSCOPY	5.04

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P52657-F1	93.50	0.91

Function

Pathways and Gene Ontology

Reactome pathways

21 pathways

ID	Pathway
R-HSA-167161	HIV Transcription Initiation
R-HSA-167162	RNA Polymerase II HIV Promoter Escape
R-HSA-167172	Transcription of the HIV genome
R-HSA-674695	RNA Polymerase II Pre-transcription Events
R-HSA-6807505	RNA polymerase II transcribes snRNA genes
R-HSA-73776	RNA Polymerase II Promoter Escape
R-HSA-73779	RNA Polymerase II Transcription Pre-Initiation And Promoter Opening
R-HSA-75953	RNA Polymerase II Transcription Initiation
R-HSA-76042	RNA Polymerase II Transcription Initiation And Promoter Clearance
R-HSA-9018519	Estrogen-dependent gene expression
R-HSA-162582	Signal Transduction
R-HSA-162587	HIV Life Cycle
R-HSA-162599	Late Phase of HIV Life Cycle
R-HSA-162906	HIV Infection
R-HSA-1643685	Disease
R-HSA-5663205	Infectious disease
R-HSA-73857	RNA Polymerase II Transcription
R-HSA-74160	Gene expression (Transcription)
R-HSA-8939211	ESR-mediated signaling
R-HSA-9006931	Signaling by Nuclear Receptors
R-HSA-9824446	Viral Infection Pathways

MSigDB gene sets: 0 (showing top):

GO Biological Process (5): transcription by RNA polymerase II (GO:0006366), transcription initiation at RNA polymerase II promoter (GO:0006367), positive regulation of transcription by RNA polymerase II (GO:0045944), RNA polymerase II preinitiation complex assembly (GO:0051123), positive regulation of transcription initiation by RNA polymerase II (GO:0060261)

GO Molecular Function (7): RNA polymerase II general transcription initiation factor binding (GO:0001091), RNA polymerase II general transcription initiation factor activity (GO:0016251), TBP-class protein binding (GO:0017025), protein homodimerization activity (GO:0042803), protein heterodimerization activity (GO:0046982), RNA polymerase II-specific DNA-binding transcription factor binding (GO:0061629), protein binding (GO:0005515)

GO Cellular Component (5): nucleus (GO:0005634), nucleoplasm (GO:0005654), transcription factor TFIID complex (GO:0005669), transcription factor TFIIA complex (GO:0005672), cytosol (GO:0005829)

Reactome top-level categories

Rollup of top-12 pathways:

Category	Pathways
RNA Polymerase II Transcription	4
Transcription of the HIV genome	2
RNA Polymerase II Transcription Initiation And Promoter Clearance	2
Late Phase of HIV Life Cycle	1
ESR-mediated signaling	1
HIV Infection	1
HIV Life Cycle	1
Viral Infection Pathways	1
Disease	1
Gene expression (Transcription)	1
Signaling by Nuclear Receptors	1
Signal Transduction	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transcription by RNA polymerase II	3
transcription initiation at RNA polymerase II promoter	2
general transcription initiation factor binding	2
protein dimerization activity	2
cellular anatomical structure	2
RNA polymerase II, holoenzyme	2
RNA polymerase II transcription regulator complex	2
DNA-templated transcription	1
DNA-templated transcription initiation	1
regulation of transcription by RNA polymerase II	1
positive regulation of DNA-templated transcription	1
transcription preinitiation complex assembly	1
positive regulation of transcription by RNA polymerase II	1
regulation of transcription initiation by RNA polymerase II	1
positive regulation of DNA-templated transcription initiation	1
RNA polymerase II complex binding	1
general transcription initiation factor activity	1
identical protein binding	1
DNA-binding transcription factor binding	1
binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cytoplasm	1

Protein interactions and networks

STRING

1530 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GTF2A2	GTF2A1	P52655	962
GTF2A2	GTF2A1L	Q9UNN4	891
GTF2A2	TBP	P20226	819
GTF2A2	STON1	Q9Y6Q2	814
GTF2A2	GTF2B	Q00403	794
GTF2A2	GTF2E1	P29083	764
GTF2A2	GTF2F1	P35269	719
GTF2A2	GTF2H1	P32780	635
GTF2A2	POLR2A	P24928	635
GTF2A2	TAF11	Q15544	515
GTF2A2	Q53S48	Q53S48	513
GTF2A2	TAF10	Q12962	508
GTF2A2	TAF13	Q15543	505
GTF2A2	CYB561D1	Q8N8Q1	500
GTF2A2	TAF9	Q16594	493

IntAct

33 interactions, top by confidence:

A	B	Type	Score
GTF2A1	GTF2A2	psi-mi:“MI:0915”(physical association)	0.940
GTF2A2	GTF2A1	psi-mi:“MI:0915”(physical association)	0.940
GTF2A1	GTF2A2	psi-mi:“MI:0407”(direct interaction)	0.940
GTF2A2	TBP	psi-mi:“MI:0407”(direct interaction)	0.800
POLR2E	POLR2D	psi-mi:“MI:0915”(physical association)	0.790
GTF2A2	TRIM7	psi-mi:“MI:0915”(physical association)	0.560
GTF2A1	INPPL1	psi-mi:“MI:0914”(association)	0.530
GTF2A2	TAF4	psi-mi:“MI:0915”(physical association)	0.490
GTF2A2	GTF2A2	psi-mi:“MI:0407”(direct interaction)	0.440
GTF2A1	GTF2A2	psi-mi:“MI:0407”(direct interaction)	0.440
GTF2A2	PTPN11	psi-mi:“MI:0915”(physical association)	0.370
GTF2A2	S100P	psi-mi:“MI:0914”(association)	0.350
GTF2A2	RP2	psi-mi:“MI:0914”(association)	0.350
GTF2A2	A2ML1	psi-mi:“MI:0914”(association)	0.350
ERCC2	POLR2D	psi-mi:“MI:0915”(physical association)	0.320
CCNH	MED19	psi-mi:“MI:0915”(physical association)	0.320
TBPL1	GTF2A2	psi-mi:“MI:0915”(physical association)	0.000
GTF2A2	TRIM7	psi-mi:“MI:0915”(physical association)	0.000
GTF2A2	GTF2A1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (36): GTF2A2 (Two-hybrid), GTF2A2 (Affinity Capture-MS), GTF2A2 (Co-fractionation), GTF2A2 (Affinity Capture-MS), GTF2A2 (Two-hybrid), TBP (Reconstituted Complex), GTF2A2 (Affinity Capture-MS), TRIM7 (Two-hybrid), GTF2A1 (Two-hybrid), TBP (Reconstituted Complex), TAF4 (Reconstituted Complex), GTF2A2 (Reconstituted Complex), GTF2A2 (Reconstituted Complex), TBPL1 (Affinity Capture-MS), GTF2A1 (Affinity Capture-MS)

ESM2 similar proteins: A0A7H0DNA6, A3DSK8, B7INA4, B7Z0L8, C4QGM3, C7ZPG2, O08950, O23624, O41126, O41252, O48398, O83053, P03516, P03538, P04028, P07266, P0C1A0, P0DSP9, P0DSQ0, P18797, P20986, P24568, P26002, P33054, P38457, P41461, P48335, P49829, P52141, P52656, P52657, P68719, P68720, P86234, Q01RT2, Q1ECJ7, Q25214, Q54EY1, Q65221, Q6C7C9

Diamond homologs: A2XZI2, A4QW40, B7Q1Q9, C4QGM3, C7ZPG2, O08950, O74948, P0CR84, P0CR85, P32774, P52656, P52657, Q0DLD3, Q39236, Q54ND1, Q5BB99, Q80ZM7, Q90YG6, Q9BIB4, Q9IA78, Q9NEX2, Q9W5B9

SIGNOR signaling

3 interactions.

A	Effect	B	Mechanism
GTF2A2	“form complex”	TFIIA	binding
RBPJ	up-regulates	GTF2A2	binding
GTF2A2	“up-regulates activity”	TBP	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 15 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
HIV Transcription Initiation	7	135.9×	4e-13
RNA Polymerase II HIV Promoter Escape	7	135.9×	4e-13
RNA Polymerase II Promoter Escape	7	135.9×	4e-13
RNA Polymerase II Transcription Pre-Initiation And Promoter Opening	7	135.9×	4e-13
RNA Polymerase II Transcription Initiation	7	135.9×	4e-13
RNA Polymerase II Transcription Initiation And Promoter Clearance	7	135.9×	4e-13
Transcription of the HIV genome	7	100.9×	3e-12
Late Phase of HIV Life Cycle	6	84.0×	7e-10

GO biological processes:

GO term	Partners	Fold	FDR
transcription initiation at RNA polymerase II promoter	5	124.8×	4e-08
transcription by RNA polymerase II	7	32.9×	4e-08

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	10
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

920 predictions. Top by Δscore:

Variant	Effect	Δscore
15:59650437:T:C	acceptor_gain	1.0000
15:59650437:T:TC	acceptor_gain	1.0000
15:59650667:AC:A	donor_gain	1.0000
15:59650668:CC:C	donor_gain	1.0000
15:59650895:T:TA	donor_gain	1.0000
15:59657423:C:A	donor_gain	1.0000
15:59642134:A:AC	donor_gain	0.9900
15:59642135:C:CC	donor_gain	0.9900
15:59642262:CCTT:C	acceptor_gain	0.9900
15:59650439:G:GC	acceptor_gain	0.9900
15:59650774:C:CC	acceptor_gain	0.9900
15:59650901:ATCT:A	donor_gain	0.9900
15:59650916:A:C	donor_gain	0.9900
15:59657422:T:TA	donor_gain	0.9900
15:59657472:A:AC	donor_gain	0.9900
15:59657473:C:CC	donor_gain	0.9900
15:59639155:TATCT:T	acceptor_loss	0.9800
15:59639157:TC:T	acceptor_loss	0.9800
15:59639158:C:CC	acceptor_gain	0.9800
15:59639158:CTA:C	acceptor_loss	0.9800
15:59639159:T:G	acceptor_loss	0.9800
15:59650439:G:C	acceptor_gain	0.9800
15:59650863:A:C	donor_gain	0.9800
15:59656959:C:CT	donor_gain	0.9800
15:59657400:CACTA:C	donor_loss	0.9800
15:59657404:AC:A	donor_loss	0.9800
15:59657405:C:CA	donor_loss	0.9800
15:59657475:T:TA	donor_gain	0.9800
15:59657482:C:CT	donor_gain	0.9800
15:59657483:C:CT	donor_gain	0.9800

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000315430 (15:59638990 A>C,G), RS1000331502 (15:59638560 G>C), RS1000399653 (15:59642754 T>C), RS1000583614 (15:59647010 T>C), RS1000821168 (15:59657413 G>C), RS1000920645 (15:59639680 G>A,C,T), RS1001172983 (15:59657508 G>A,T), RS1001263256 (15:59639753 T>G), RS1001436320 (15:59655161 C>T), RS1001487996 (15:59654959 T>G), RS1001532401 (15:59638301 C>T), RS1001584780 (15:59638159 C>G,T), RS1001739632 (15:59649340 T>C), RS1001855375 (15:59645867 T>C), RS1002084486 (15:59646240 A>C)

Disease associations

OMIM: gene MIM:600519 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST006976_117	Macular thickness	2.000000e-11

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases methylation, increases expression	3
bisphenol A	decreases expression, increases expression	2
Air Pollutants	affects expression, increases abundance, decreases expression	2
bufotalin	increases expression	1
beta-lapachone	increases expression	1
arsenite	affects binding, increases reaction	1
sodium arsenite	affects expression	1
di-n-butylphosphoric acid	affects expression	1
chloropicrin	affects expression	1
tanespimycin	increases expression	1
nickel acetate	affects expression	1
Grape Seed Proanthocyanidins	affects cotreatment, increases expression	1
MT19c compound	increases expression	1
Benzo(a)pyrene	increases methylation	1
Catechin	affects cotreatment, increases expression	1
Doxorubicin	increases expression	1
Formaldehyde	increases expression	1
Ivermectin	decreases expression	1
Lead	affects expression	1
Ozone	affects expression, increases abundance	1
Rotenone	increases expression	1
Smoke	decreases expression	1
Testosterone	decreases expression	1
Tretinoin	decreases expression	1
Lactic Acid	decreases expression	1
Acrylamide	increases expression	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_GZ87	K562 eGFP-GTF2A2	Cancer cell line	Female

Clinical trials (associated diseases)

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