GGT2P

gamma-glutamyltransferase 2, pseudogene, the group of Gamma-glutamyltransferases

Basic information

Region (hg38): 22:21207973-21225554

Previous symbols: [ "GGT", "GGT2" ]

Links

ENSG00000133475 ∙ NCBI:728441 ∙ OMIM:137181 ∙ HGNC:4251 ∙ Uniprot:P36268 ∙ 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 GGT2P gene.

• not provided (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GGT2P 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				3		3
splice region						0
non coding				6		6
Total	0	0	0	9	0

Variants in GGT2P

This is a list of pathogenic ClinVar variants found in the GGT2P region.

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

Position	Type	Phenotype	Significance	ClinVar
22-21208865-C-T			Likely benign (Mar 01, 2023)
22-21208901-G-A			Likely benign (Dec 01, 2023)
22-21209102-C-T			Likely benign (May 01, 2022)
22-21215926-A-G			Likely benign (Aug 01, 2023)
22-21221927-G-T			Likely benign (Aug 01, 2023)
22-21222187-T-C			Likely benign (Jul 01, 2023)
22-21222199-G-A			Likely benign (Jul 01, 2023)
22-21225468-G-A			Likely benign (Apr 01, 2023)
22-21225471-C-T			Likely benign (Oct 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GGT2P	protein_coding	protein_coding	ENST00000401924	12	19665

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000130	0.649	118592	1	17	118610	0.0000759

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.239	117	125	0.940	0.00000695	3501
Missense in Polyphen		36	44.66	0.80609		1269
Synonymous	1.05	44	53.8	0.818	0.00000312	1150
Loss of Function	0.789	7	9.65	0.726	4.47e-7	254

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00101	0.000924
Finnish	0.0000484	0.0000473
European (Non-Finnish)	0.00000947	0.00000917
Middle Eastern	0.00101	0.000924
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Isoform 1, isoform 2 and isoform 3 lack catalytic activity due to its inability to undergo the autocatalytic cleavage needed to produce a mature, enzymatically active heterodimer. {ECO:0000269|PubMed:23682772}.
• Pathway: Busulfan Pathway, Pharmacodynamics;Glutathione conjugation;Metabolism of lipids;Phase II - Conjugation of compounds;Prostaglandin Leukotriene metabolism;Synthesis of Leukotrienes (LT) and Eoxins (EX);Arachidonic acid metabolism;Biological oxidations;Metabolism;Fatty acid metabolism;Glutathione synthesis and recycling;Aflatoxin activation and detoxification (Consensus)

Recessive Scores

• pRec: 0.117

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.290
• ghis: 0.472

Essentials

• gene_indispensability_pred: N
• gene_indispensability_score: 0.164

Gene Damage Prediction

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

Gene ontology

• Biological process: regulation of immune system process;translation;cellular amino acid metabolic process;glutamate metabolic process;glutathione metabolic process;glutathione catabolic process;spermatogenesis;cysteine biosynthetic process;peptide modification;zymogen activation;response to estradiol;response to lipopolysaccharide;response to tumor necrosis factor;regulation of inflammatory response;leukotriene D4 biosynthetic process
• Cellular component: endoplasmic reticulum;perinuclear region of cytoplasm;extracellular exosome
• Molecular function: peptidyltransferase activity;glutathione hydrolase activity