GABPB2

protein-coding

GA binding protein transcription factor subunit beta 2, the group of Ankyrin repeat domain containing

Gene summary

Enables transcription cis-regulatory region binding activity. Acts upstream of or within positive regulation of transcription by RNA polymerase II. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_144618.3

Inheritance

—

ClinVar variants

U:65B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.54

Max pathogenic AF

—

Genomic locus

chr1:151,070,578-151,125,542

External References & Databases

Ensembl (ENSG00000143458)

Transcript & Mutation Effects

hg38 • Region Span ~55.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GABPB2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 64

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_144618.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			61 clinvar	3 clinvar		64
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	65	3	0	68

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 49 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_144618.3	RefSeq	NP_653219.1	8	MANE Select
ENST00000368918.8	Ensembl	ENSP00000357914.3	8	MANE Select
NM_001323906.2	RefSeq	NP_001310835.1	9	Standard
NM_001323907.2	RefSeq	NP_001310836.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

positive regulation of transcription by RNA polymerase II

Molecular Function

protein binding
protein homodimerization activity
transcription regulatory region DNA binding
protein heterodimerization activity

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000368918
Coding exons: 8
Length: 54965
Individuals with no LoFs: 125688
Homozygous LoFs: 0
Heterozygous LoFs: 59
Defined: 125747
p: 0.000235

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.846	206	243	0.847	0.0000123	2884
Missense (PolyPhen)		41	53.831	0.76164		637
Synonymous	1.04	79	91.7	0.861	0.00000477	929
Loss of Function	1.99	12	22.1	0.542	0.00000131	238

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00014	0.00012	rare
Latino/Admixed American	0.00036	0.00035	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00033	0.00033	rare
Finnish	0.00042	0.00042	rare
European (Non-Finnish)	0.00021	0.00021	rare
South Asian	0.00016	0.00016	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May function as transcription factor capable of interacting with purine rich repeats (GA repeats). {ECO:0000250}.;

Recessive Scores

pRec: 0.0976

Intolerance Scores

LoFtool: 0.820
RVIS EVS: 0.26
RVIS percentile EVS: 70.44

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.481

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium