GABPB2

Summary

GABPB2 (GA binding protein transcription factor subunit beta 2, HGNC:28441) is a protein-coding gene on chromosome 1q21.3, encoding GA-binding protein subunit beta-2 (Q8TAK5). May function as transcription factor capable of interacting with purine rich repeats (GA repeats).

Enables transcription cis-regulatory region binding activity. Acts upstream of or within positive regulation of transcription by RNA polymerase II. Located in nucleus.

Source: NCBI Gene 126626 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 74 total
• MANE Select transcript: NM_144618

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28441
Approved symbol	GABPB2
Name	GA binding protein transcription factor subunit beta 2
Location	1q21.3
Locus type	gene with protein product
Status	Approved
Aliases	MGC29891
Ensembl gene	ENSG00000143458
Ensembl biotype	protein_coding
OMIM	621284
Entrez	126626

Gene structure

Transcript identifiers

Ensembl transcripts: 25 — 21 protein_coding, 4 protein_coding_CDS_not_defined

ENST00000368916, ENST00000368918, ENST00000462520, ENST00000467551, ENST00000486076, ENST00000489549, ENST00000897348, ENST00000897349, ENST00000897350, ENST00000897351, ENST00000897352, ENST00000897353, ENST00000931883, ENST00000931884, ENST00000947109, ENST00000947110, ENST00000947111, ENST00000947112, ENST00000947113, ENST00000947114, ENST00000947115, ENST00000947116, ENST00000947117, ENST00000947118, ENST00000947119

RefSeq mRNA: 9 — MANE Select: NM_144618 NM_001323906, NM_001323907, NM_001323908, NM_001323909, NM_001323910, NM_001323911, NM_001323912, NM_001323913, NM_144618

CCDS: CCDS81373, CCDS983

Canonical transcript exons

ENST00000368918 — 9 exons

Exon	Start	End
ENSE00001150300	151117392	151117516
ENSE00001291221	151070761	151070934
ENSE00001897197	151117957	151125542
ENSE00003472297	151088190	151088297
ENSE00003486604	151107037	151107222
ENSE00003594567	151097852	151098002
ENSE00003657622	151103562	151103675
ENSE00003668156	151090406	151090573
ENSE00003671254	151093192	151093386

Expression profiles

Bgee: expression breadth ubiquitous, 248 present calls, max score 92.06.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.1993 / max 271.3708, expressed in 1625 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
5201	2.6020	1286
5202	1.6831	817
5203	0.9984	468
5200	0.9158	536

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
oviduct epithelium	UBERON:0004804	92.06	gold quality
ileal mucosa	UBERON:0000331	89.52	gold quality
thymus	UBERON:0002370	88.86	gold quality
tibialis anterior	UBERON:0001385	88.83	silver quality
calcaneal tendon	UBERON:0003701	88.02	gold quality
tibia	UBERON:0000979	87.83	gold quality
upper arm skin	UBERON:0004263	87.38	gold quality
pancreatic ductal cell	CL:0002079	86.99	silver quality
tendon	UBERON:0000043	86.73	gold quality
esophagus squamous epithelium	UBERON:0006920	85.23	gold quality
epithelium of nasopharynx	UBERON:0001951	84.91	gold quality
cardiac muscle of right atrium	UBERON:0003379	84.91	gold quality
sural nerve	UBERON:0015488	84.68	gold quality
germinal epithelium of ovary	UBERON:0001304	84.58	gold quality
kidney epithelium	UBERON:0004819	83.57	silver quality
gingival epithelium	UBERON:0001949	83.15	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.09	gold quality
parietal pleura	UBERON:0002400	83.06	gold quality
testis	UBERON:0000473	82.75	gold quality
trabecular bone tissue	UBERON:0002483	82.69	gold quality
corpus callosum	UBERON:0002336	82.63	gold quality
left testis	UBERON:0004533	82.57	gold quality
layer of synovial tissue	UBERON:0007616	82.54	gold quality
right testis	UBERON:0004534	82.46	gold quality
colonic epithelium	UBERON:0000397	82.12	gold quality
left ventricle myocardium	UBERON:0006566	82.07	silver quality
fallopian tube	UBERON:0003889	82.00	gold quality
bone marrow cell	CL:0002092	81.67	gold quality
ovary	UBERON:0000992	81.48	gold quality
popliteal artery	UBERON:0002250	81.19	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	9.50

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

Target	Regulation
RPS3A	Unknown

Upstream regulators (CollecTRI, top): RELA

miRNA regulators (miRDB)

34 targeting GABPB2, 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-LET-7A-3P	100.00	74.03	3932
HSA-MIR-9-3P	99.96	70.88	2068
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-3682-5P	99.93	67.97	1163
HSA-MIR-6835-3P	99.93	70.49	2904
HSA-MIR-10523-5P	99.91	69.22	2038
HSA-MIR-454-3P	99.91	74.01	1925
HSA-MIR-130A-3P	99.90	73.31	1861
HSA-MIR-130B-3P	99.90	73.27	1850
HSA-MIR-301A-3P	99.90	73.15	1839
HSA-MIR-301B-3P	99.90	73.19	1836
HSA-MIR-3666	99.90	73.24	1833
HSA-MIR-4295	99.90	73.11	1838
HSA-MIR-4659A-3P	99.80	72.62	4248
HSA-MIR-4659B-3P	99.80	72.62	4248
HSA-MIR-4517	99.76	69.19	1867
HSA-MIR-148A-3P	99.74	73.77	1700
HSA-MIR-148B-3P	99.74	73.75	1700
HSA-MIR-152-3P	99.74	73.75	1703
HSA-MIR-4422	99.72	72.07	2908
HSA-MIR-1200	99.71	70.42	1838
HSA-MIR-6740-3P	99.48	68.49	1392
HSA-MIR-3182	99.40	68.15	2454
HSA-MIR-135A-5P	99.36	71.85	1601
HSA-MIR-135B-5P	99.36	71.63	1613
HSA-MIR-133A-3P	99.27	71.53	1270
HSA-MIR-133B	99.27	71.53	1270
HSA-MIR-3908	98.75	67.31	1160
HSA-MIR-583	98.71	67.44	1791
HSA-MIR-3159	97.94	66.79	1098

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	gabpb2b	ENSDARG00000054344
mus_musculus	Gabpb2	ENSMUSG00000038766
rattus_norvegicus	Gabpb2	ENSRNOG00000021105
drosophila_melanogaster	Atac3	FBGN0052343

Paralogs (2): GABPB1 (ENSG00000104064), IQANK1 (ENSG00000203499)

Protein

Protein identifiers

GA-binding protein subunit beta-2 — Q8TAK5 (reviewed: Q8TAK5)

All UniProt accessions (2): Q8TAK5, Q5SZG2

UniProt curated annotations — full annotation on UniProt →

Function. May function as transcription factor capable of interacting with purine rich repeats (GA repeats).

Subunit / interactions. Heterotetramer of two alpha and two beta subunits. The C-terminal is necessary for the formation of a heterotetrameric GABP-alpha-2/beta-2 complex, and also facilitates homotypic dimerization. Interacts with ADGRB2.

Subcellular location. Nucleus.

RefSeq proteins (9): NP_001310835, NP_001310836, NP_001310837, NP_001310838, NP_001310839, NP_001310840, NP_001310841, NP_001310842, NP_653219* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002110	Ankyrin_rpt	Repeat
IPR036770	Ankyrin_rpt-contain_sf	Homologous_superfamily
IPR050663	Ankyrin-SOCS_Box	Family

Pfam: PF12796

UniProt features (15 total): repeat 5, compositionally biased region 2, sequence conflict 2, region of interest 2, chain 1, modified residue 1, sequence variant 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8TAK5-F1	64.02	0.40

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): 256

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 162 (showing top): SWEET_KRAS_ONCOGENIC_SIGNATURE, AAGCCAT_MIR135A_MIR135B, MAZ_Q6, IVANOVA_HEMATOPOIESIS_MATURE_CELL, CAGCTG_AP4_Q5, GTGCCTT_MIR506, NFKB_C, ATTCTTT_MIR186, ATGCTGG_MIR338, CHIANG_LIVER_CANCER_SUBCLASS_INTERFERON_DN, ATCATGA_MIR433, FISCHER_DREAM_TARGETS, MARTINEZ_RESPONSE_TO_TRABECTEDIN_DN, TGGAAA_NFAT_Q4_01, BOYLAN_MULTIPLE_MYELOMA_C_D_UP

GO Biological Process (1): positive regulation of transcription by RNA polymerase II (GO:0045944)

GO Molecular Function (3): transcription cis-regulatory region binding (GO:0000976), identical protein binding (GO:0042802), protein binding (GO:0005515)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of transcription by RNA polymerase II	1
transcription by RNA polymerase II	1
positive regulation of DNA-templated transcription	1
transcription regulatory region nucleic acid binding	1
sequence-specific double-stranded DNA binding	1
protein binding	1
binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

1114 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GABPB2	GABPA	Q06546	542
GABPB2	M0QYU9	M0QYU9	476
GABPB2	SMIM7	Q9BQ49	470
GABPB2	CLASRP	Q8N2M8	350
GABPB2	CCDC90B	Q9GZT6	349
GABPB2	NBPF9	P0DPF3	323
GABPB2	RHEBL1	Q8TAI7	318
GABPB2	MLLT11	Q13015	302
GABPB2	ARHGEF38	Q9NXL2	289
GABPB2	ETV4	P43268	273
GABPB2	GLT1D1	Q96MS3	270
GABPB2	ZNF124	Q15973	270
GABPB2	CMSS1	Q9BQ75	270
GABPB2	ELK4	P28323	262
GABPB2	GOLPH3L	Q9H4A5	258

IntAct

39 interactions, top by confidence:

A	B	Type	Score
GABPB2	GABPA	psi-mi:“MI:0915”(physical association)	0.770
GABPA	GABPB2	psi-mi:“MI:0915”(physical association)	0.770
GABPB2	GORASP2	psi-mi:“MI:0915”(physical association)	0.720
GORASP2	GABPB2	psi-mi:“MI:0915”(physical association)	0.720
GABPA	GABPB1	psi-mi:“MI:0914”(association)	0.700
SNRPB2	GABPB2	psi-mi:“MI:0915”(physical association)	0.560
VAC14	GABPB2	psi-mi:“MI:0915”(physical association)	0.560
LONRF1	GABPB2	psi-mi:“MI:0915”(physical association)	0.560
TSEN2	GABPB2	psi-mi:“MI:0915”(physical association)	0.560
GABPB2	FLNA	psi-mi:“MI:0915”(physical association)	0.560
PIAS4	GABPB2	psi-mi:“MI:0915”(physical association)	0.560
GABPB2	CRK	psi-mi:“MI:0915”(physical association)	0.490
CRK	GABPB2	psi-mi:“MI:0915”(physical association)	0.490
GABPB2	HIF1AN	psi-mi:“MI:0210”(hydroxylation reaction)	0.440
GABPB2	PLCG2	psi-mi:“MI:0915”(physical association)	0.370
GABPB2	E7	psi-mi:“MI:0915”(physical association)	0.370
KDM1A	GABPB2	psi-mi:“MI:0915”(physical association)	0.370
GABPB2	ZDHHC17	psi-mi:“MI:0915”(physical association)	0.370
GABPB2	VAC14	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (20): GABPB2 (Two-hybrid), GABPB2 (Two-hybrid), GABPB2 (Two-hybrid), GABPB2 (Two-hybrid), GABPA (Affinity Capture-MS), GABPB2 (Affinity Capture-MS), GABPB2 (Two-hybrid), GABPB2 (Two-hybrid), GABPB2 (Two-hybrid), LONRF1 (Two-hybrid), GABPA (Two-hybrid), TSEN2 (Two-hybrid), GABPB2 (Affinity Capture-RNA), GABPA (Affinity Capture-MS), GABPB2 (Two-hybrid)

ESM2 similar proteins: A6QQW0, B4F7E9, O15391, O43167, O62836, O70230, O70494, P08048, P15337, P17010, P17012, P18846, P20385, P25490, P27699, P36508, P52747, P79145, P81069, P81269, Q00420, Q00899, Q01147, Q01611, Q02447, Q03060, Q03061, Q06547, Q08DA8, Q0V8G2, Q1LYE3, Q1LZH5, Q1RMI3, Q4V8R6, Q52KB5, Q52V16, Q58DZ6, Q5XIU2, Q66K89, Q6B4Z5

Diamond homologs: P81069, Q00420, Q06547, Q0V8G2, Q1RMI3, Q69ZU8, Q8TAK5, Q9Y2G4

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
GABPB2	“down-regulates activity”	HCFC1	binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	61
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2047 predictions. Top by Δscore:

Variant	Effect	Δscore
1:151088181:T:G	acceptor_gain	1.0000
1:151093187:GACA:G	acceptor_loss	1.0000
1:151093188:ACAG:A	acceptor_loss	1.0000
1:151093189:CA:C	acceptor_loss	1.0000
1:151093190:A:AG	acceptor_gain	1.0000
1:151093190:AGAAT:A	acceptor_gain	1.0000
1:151093191:G:GA	acceptor_gain	1.0000
1:151093191:GA:G	acceptor_gain	1.0000
1:151093191:GAAT:G	acceptor_gain	1.0000
1:151093191:GAATG:G	acceptor_gain	1.0000
1:151093383:CCAG:C	donor_loss	1.0000
1:151093384:CAGG:C	donor_loss	1.0000
1:151093386:GGTGT:G	donor_loss	1.0000
1:151093387:GTGTG:G	donor_loss	1.0000
1:151107035:A:AG	acceptor_gain	1.0000
1:151107036:G:GG	acceptor_gain	1.0000
1:151107036:GC:G	acceptor_gain	1.0000
1:151107036:GCC:G	acceptor_gain	1.0000
1:151107036:GCCA:G	acceptor_gain	1.0000
1:151107036:GCCAA:G	acceptor_gain	1.0000
1:151107218:GCAAG:G	donor_gain	1.0000
1:151107219:CAAGG:C	donor_loss	1.0000
1:151107220:AAGGT:A	donor_loss	1.0000
1:151107221:AGGTG:A	donor_loss	1.0000
1:151107223:G:GA	donor_loss	1.0000
1:151107224:T:G	donor_loss	1.0000
1:151117390:A:AG	acceptor_gain	1.0000
1:151117391:G:GA	acceptor_gain	1.0000
1:151117391:GTT:G	acceptor_gain	1.0000
1:151117391:GTTCT:G	acceptor_gain	1.0000

AlphaMissense

2896 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:151090419:C:A	P41H	0.999
1:151090422:T:A	L42H	0.999
1:151090428:T:C	L44P	0.999
1:151090434:C:A	A46D	0.999
1:151090467:T:C	L57P	0.999
1:151090470:T:C	L58P	0.999
1:151090518:C:A	P74H	0.999
1:151090566:T:C	L90P	0.999
1:151093216:G:C	D101H	0.999
1:151093217:A:T	D101V	0.999
1:151093283:T:C	L123P	0.999
1:151088226:G:C	A13P	0.998
1:151088283:T:C	F32L	0.998
1:151088285:C:A	F32L	0.998
1:151088285:C:G	F32L	0.998
1:151088293:A:T	D35V	0.998
1:151090422:T:C	L42P	0.998
1:151090433:G:C	A46P	0.998
1:151090443:G:T	G49V	0.998
1:151090457:G:C	A54P	0.998
1:151090467:T:A	L57H	0.998
1:151090500:C:T	T68I	0.998
1:151090518:C:G	P74R	0.998
1:151090521:T:C	L75S	0.998
1:151090521:T:G	L75W	0.998
1:151090529:G:C	A78P	0.998
1:151090530:C:A	A78D	0.998
1:151090532:G:C	A79P	0.998
1:151090542:G:T	G82V	0.998
1:151090563:T:C	L89P	0.998

dbSNP variants (sampled 300 via entrez): RS1000052352 (1:151080571 G>A), RS1000082523 (1:151094136 C>T), RS1000101679 (1:151086793 G>A), RS1000140490 (1:151069110 C>T), RS1000156130 (1:151071936 C>T), RS1000220535 (1:151117570 G>A,T), RS1000281806 (1:151107823 C>G), RS1000287154 (1:151093129 T>C), RS1000386746 (1:151100310 A>G), RS1000515712 (1:151106369 G>A,T), RS1000558759 (1:151114311 C>T), RS1000598719 (1:151089206 G>A,T), RS1000673480 (1:151083853 G>T), RS1000689592 (1:151070437 C>A), RS1000705977 (1:151083615 CAG>C)

Disease associations

OMIM: gene MIM:621284 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST005951_38	Body mass index	4.000000e-09
GCST90000025_768	Appendicular lean mass	5.000000e-15
GCST90000047_16	Age at first sexual intercourse	2.000000e-09

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0004980	appendicular lean mass
EFO:0009749	age at first sexual intercourse 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 cotreatment, decreases expression, increases abundance, increases expression	2
Estradiol	decreases expression, increases expression	2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	2
triphenyl phosphate	affects expression	1
bisphenol A	increases expression	1
hydroxyhydroquinone	increases expression	1
sulforaphane	increases expression	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
benzo(e)pyrene	increases methylation	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	increases expression, affects cotreatment	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
chloropicrin	increases expression	1
erucylphospho-N,N,N-trimethylpropylammonium	increases expression	1
abrine	increases expression	1
(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)	increases expression	1
MT19c compound	increases 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	increases expression	1
Sunitinib	increases expression	1
Arsenic Trioxide	decreases expression	1
Arsenic	affects cotreatment, decreases expression, increases abundance	1
Coumestrol	affects cotreatment, increases expression	1
Hydrogen Peroxide	affects expression	1
Manganese	affects cotreatment, decreases expression, increases abundance	1
Methapyrilene	increases methylation	1
Quercetin	increases expression	1
Valproic Acid	decreases expression	1
Vitamin E	decreases expression	1
Cyclosporine	increases expression	1
Copper Sulfate	increases expression	1

Clinical trials (associated diseases)

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