GABPB2

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

Basic information

Region (hg38): 1:151070578-151125542

Links

ENSG00000143458 ∙ NCBI:126626 ∙ ∙ HGNC:28441 ∙ Uniprot:Q8TAK5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GABPB2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GABPB2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			35	2		37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	2	0

Variants in GABPB2

This is a list of pathogenic ClinVar variants found in the GABPB2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-151088194-C-A		not specified	Uncertain significance (Jun 05, 2024)
1-151088289-A-G		not specified	Uncertain significance (May 12, 2024)
1-151088290-C-T		not specified	Uncertain significance (Oct 16, 2024)
1-151090473-G-A		not specified	Uncertain significance (Aug 02, 2021)
1-151090485-G-T		not specified	Uncertain significance (Nov 18, 2022)
1-151090502-A-G		not specified	Uncertain significance (May 04, 2023)
1-151090517-C-T		not specified	Uncertain significance (Aug 13, 2021)
1-151090538-G-A		not specified	Uncertain significance (Dec 19, 2023)
1-151090548-C-T		not specified	Uncertain significance (Feb 21, 2024)
1-151090553-A-G		not specified	Uncertain significance (May 08, 2024)
1-151090571-C-T		not specified	Uncertain significance (Oct 01, 2024)
1-151093223-T-A		not specified	Uncertain significance (Oct 03, 2023)
1-151093256-G-A		not specified	Likely benign (Jul 08, 2022)
1-151093273-G-A		not specified	Uncertain significance (May 30, 2024)
1-151093292-A-G		not specified	Uncertain significance (Dec 04, 2024)
1-151093328-A-G		not specified	Uncertain significance (Sep 23, 2023)
1-151097853-A-G		not specified	Uncertain significance (Dec 20, 2023)
1-151097862-A-G		not specified	Uncertain significance (Dec 05, 2022)
1-151097897-C-T		not specified	Uncertain significance (Nov 07, 2024)
1-151097954-G-A		not specified	Uncertain significance (Jan 04, 2022)
1-151097976-C-G		not specified	Uncertain significance (Sep 12, 2023)
1-151097990-A-G		not specified	Uncertain significance (Sep 03, 2024)
1-151103574-C-T		not specified	Uncertain significance (Oct 05, 2023)
1-151103594-A-G		not specified	Uncertain significance (Sep 10, 2024)
1-151103600-A-G		not specified	Uncertain significance (Sep 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GABPB2	protein_coding	protein_coding	ENST00000368918	8	54965

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000541	0.970	125688	0	59	125747	0.000235

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.846	206	243	0.847	0.0000123	2884
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000494	0.000479
Ashkenazi Jewish	0.00	0.00
East Asian	0.000330	0.000326
Finnish	0.000416	0.000416
European (Non-Finnish)	0.000212	0.000211
Middle Eastern	0.000330	0.000326
South Asian	0.000165	0.000163
Other	0.000163	0.000163

dbNSFP

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

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.280
• ghis: 0.485

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.481

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gabpb2
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: protein binding;protein homodimerization activity;transcription regulatory region DNA binding;protein heterodimerization activity