GABPA

GA binding protein transcription factor subunit alpha, the group of ETS transcription factor family

Basic information

Region (hg38): 21:25734570-25772460

Links

ENSG00000154727 ∙ NCBI:2551 ∙ OMIM:600609 ∙ HGNC:4071 ∙ Uniprot:Q06546 ∙ 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 GABPA gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GABPA 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					2	2
missense			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	0	2

Variants in GABPA

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

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

Position	Type	Phenotype	Significance	ClinVar
21-25745223-A-G		not specified	Uncertain significance (Jun 13, 2024)
21-25745266-A-G		not specified	Uncertain significance (Jan 03, 2024)
21-25749115-A-T		not specified	Uncertain significance (Oct 20, 2024)
21-25752006-A-G		not specified	Uncertain significance (Dec 20, 2021)
21-25752031-C-T		not specified	Uncertain significance (Nov 08, 2022)
21-25752036-A-G		not specified	Uncertain significance (Dec 04, 2024)
21-25752141-A-G		not specified	Uncertain significance (Dec 09, 2024)
21-25752180-G-T		not specified	Uncertain significance (Dec 15, 2023)
21-25752218-C-T			Benign (Jan 05, 2018)
21-25752227-A-G		not specified	Uncertain significance (May 01, 2023)
21-25758033-C-G		not specified	Uncertain significance (Nov 09, 2022)
21-25758072-A-G		not specified	Uncertain significance (Apr 09, 2024)
21-25758082-A-C		not specified	Uncertain significance (Aug 28, 2023)
21-25758109-C-T		not specified	Uncertain significance (Jan 10, 2023)
21-25758171-A-T		not specified	Uncertain significance (Aug 22, 2023)
21-25764221-A-C		not specified	Uncertain significance (Jun 23, 2023)
21-25764234-T-C		not specified	Uncertain significance (Feb 15, 2023)
21-25764236-C-A		not specified	Uncertain significance (Aug 02, 2023)
21-25764278-G-A		not specified	Uncertain significance (Jun 16, 2023)
21-25764303-C-T		not specified	Uncertain significance (Dec 27, 2023)
21-25764304-G-A			Benign (Dec 20, 2017)
21-25764649-A-G		not specified	Uncertain significance (Apr 15, 2024)
21-25769203-G-T		not specified	Uncertain significance (Nov 02, 2023)
21-25769216-C-T		not specified	Uncertain significance (Jul 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GABPA	protein_coding	protein_coding	ENST00000354828	9	37891

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00188	119644	0	3	119647	0.0000125

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.12	108	246	0.439	0.0000129	2979
Missense in Polyphen		16	70.572	0.22672		988
Synonymous	-0.664	92	84.2	1.09	0.00000457	849
Loss of Function	4.47	2	27.1	0.0737	0.00000149	296

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000336	0.0000336
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000186	0.0000181
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor capable of interacting with purine rich repeats (GA repeats). Necessary for the expression of the Adenovirus E4 gene.
• Pathway: Energy Metabolism;Allograft Rejection;Myometrial Relaxation and Contraction Pathways;Mitochondrial biogenesis;Hematopoietic Stem Cell Gene Regulation by GABP alpha-beta Complex;Mitochondrial Gene Expression;Transcriptional activation of mitochondrial biogenesis;Mitochondrial biogenesis;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.191

Intolerance Scores

• rvis_EVS: -0.41
• rvis_percentile_EVS: 26.23

Haploinsufficiency Scores

• pHI: 0.152
• hipred: Y
• hipred_score: 0.783
• ghis: 0.698

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gabpa
• Phenotype: endocrine/exocrine gland phenotype; growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;blastocyst formation;regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;mitochondrion organization;positive regulation of gene expression;cell differentiation;negative regulation of megakaryocyte differentiation;positive regulation of transcription by RNA polymerase II;cellular response to dopamine
• Cellular component: nuclear chromatin;nucleus;nucleoplasm
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA binding;chromatin binding;DNA-binding transcription factor activity;transcription coactivator activity;protein binding;activating transcription factor binding;transcription regulatory region DNA binding;protein heterodimerization activity