GPT

glutamic--pyruvic transaminase

Basic information

Region (hg38): 8:144502973-144507174

Links

ENSG00000167701 ∙ NCBI:2875 ∙ OMIM:138200 ∙ HGNC:4552 ∙ Uniprot:P24298 ∙ 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 GPT gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPT 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				8	2	10
missense			54	9	2	65
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region					1	1
non coding				2		2
Total	0	0	55	19	4

Variants in GPT

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

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

Position	Type	Phenotype	Significance	ClinVar
8-144504326-C-T		not specified	Uncertain significance (Aug 26, 2024)
8-144504336-C-A			Likely benign (Dec 31, 2019)
8-144504339-T-A		not specified	Uncertain significance (Oct 27, 2023)
8-144504344-C-G		GPT POLYMORPHISM	Benign (Mar 01, 1997)
8-144504390-G-A		not specified	Uncertain significance (Nov 14, 2024)
8-144504396-G-A		not specified	Uncertain significance (Feb 27, 2023)
8-144504414-T-C		not specified	Uncertain significance (Oct 27, 2021)
8-144504417-G-A		not specified	Uncertain significance (Jul 12, 2022)
8-144504462-G-A		not specified	Uncertain significance (Apr 27, 2022)
8-144504615-G-A			Likely benign (Jun 08, 2018)
8-144504634-C-T		not specified	Uncertain significance (Dec 13, 2022)
8-144504646-G-A		not specified	Uncertain significance (Jan 23, 2024)
8-144504672-G-A			Benign (Oct 24, 2018)
8-144504703-C-T			Likely benign (Dec 31, 2019)
8-144504778-C-T		not specified	Uncertain significance (Apr 24, 2024)
8-144504798-C-T		not specified	Uncertain significance (Jun 05, 2024)
8-144504824-C-T			Likely benign (Feb 08, 2018)
8-144504838-G-A			Benign (Dec 31, 2019)
8-144504845-G-A			Likely benign (Dec 31, 2019)
8-144504847-G-A		not specified	Uncertain significance (Jun 05, 2023)
8-144505004-A-G		not specified	Uncertain significance (Nov 06, 2024)
8-144505009-G-A		not specified	Likely benign (Apr 24, 2024)
8-144505017-C-T			Likely benign (May 11, 2018)
8-144505077-C-T			Likely benign (Mar 09, 2018)
8-144505129-G-A		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPT	protein_coding	protein_coding	ENST00000394955	11	4202

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.59e-19	0.000676	125583	0	144	125727	0.000573

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.00	387	335	1.15	0.0000261	3161
Missense in Polyphen		170	136.41	1.2462		1329
Synonymous	-3.62	205	149	1.38	0.0000124	1031
Loss of Function	-0.757	26	22.2	1.17	0.00000106	240

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000519	0.000508
Ashkenazi Jewish	0.000108	0.0000992
East Asian	0.00126	0.00125
Finnish	0.0000989	0.0000924
European (Non-Finnish)	0.000796	0.000730
Middle Eastern	0.00126	0.00125
South Asian	0.000654	0.000653
Other	0.000352	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the reversible transamination between alanine and 2-oxoglutarate to form pyruvate and glutamate. Participates in cellular nitrogen metabolism and also in liver gluconeogenesis starting with precursors transported from skeletal muscles (By similarity). {ECO:0000250}.
• Pathway: Alanine, aspartate and glutamate metabolism - Homo sapiens (human);Arginine biosynthesis - Homo sapiens (human);Pyruvate Carboxylase Deficiency;Primary Hyperoxaluria Type I;Argininemia;2-Hydroxyglutric Aciduria (D And L Form);Lactic Acidemia;Citrullinemia Type I;Carbamoyl Phosphate Synthetase Deficiency;Argininosuccinic Aciduria;Glucose-Alanine Cycle;Alanine Metabolism;Urea Cycle;Homocarnosinosis;Hyperinsulinism-Hyperammonemia Syndrome;Succinic semialdehyde dehydrogenase deficiency;Ornithine Transcarbamylase Deficiency (OTC Deficiency);4-Hydroxybutyric Aciduria/Succinic Semialdehyde Dehydrogenase Deficiency;Glutamate Metabolism;Alanine and aspartate metabolism;Cori Cycle;Alanine Aspartate Asparagine metabolism;Glutamate Glutamine metabolism;Metabolism of amino acids and derivatives;Glycolysis Gluconeogenesis;Metabolism;alanine biosynthesis/degradation;Amino acid synthesis and interconversion (transamination) (Consensus)

Recessive Scores

• pRec: 0.815

Intolerance Scores

• loftool: 0.430
• rvis_EVS: 0.29
• rvis_percentile_EVS: 71.6

Haploinsufficiency Scores

• pHI: 0.137
• hipred: N
• hipred_score: 0.284
• ghis: 0.427

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.230

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpt
• Phenotype: skeleton phenotype

Gene ontology

• Biological process: cellular amino acid biosynthetic process;L-alanine catabolic process
• Cellular component: cytosol;extracellular exosome
• Molecular function: L-alanine:2-oxoglutarate aminotransferase activity;pyridoxal phosphate binding