GGCT

gamma-glutamylcyclotransferase

Basic information

Region (hg38): 7:30496621-30504841

Previous symbols: [ "C7orf24", "GCTG" ]

Links

ENSG00000006625 ∙ NCBI:79017 ∙ OMIM:137170 ∙ HGNC:21705 ∙ Uniprot:O75223 ∙ 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 GGCT gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GGCT 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				1		1
missense			12	1	1	14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	2	1

Variants in GGCT

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

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

Position	Type	Phenotype	Significance	ClinVar
7-30497160-C-T		not specified	Uncertain significance (Dec 19, 2022)
7-30497171-A-T		not specified	Uncertain significance (Sep 06, 2024)
7-30497192-T-C		not specified	Uncertain significance (Mar 19, 2024)
7-30497200-C-T			Benign (Mar 29, 2018)
7-30498826-G-A		not specified	Uncertain significance (Jul 17, 2024)
7-30498834-T-C		not specified	Uncertain significance (Feb 28, 2024)
7-30500537-C-T		not specified	Likely benign (Jul 30, 2024)
7-30500545-G-T		not specified	Uncertain significance (Dec 11, 2024)
7-30500599-G-A		not specified	Uncertain significance (Oct 26, 2021)
7-30500641-C-T		not specified	Uncertain significance (Dec 11, 2024)
7-30500656-G-C		not specified	Uncertain significance (Dec 02, 2024)
7-30504583-C-T		not specified	Uncertain significance (Jan 03, 2022)
7-30504606-T-C		not specified	Uncertain significance (Oct 05, 2023)
7-30504615-T-G		not specified	Uncertain significance (Jan 10, 2023)
7-30504643-C-T		not specified	Uncertain significance (Jun 02, 2024)
7-30504699-G-C		not specified	Uncertain significance (Jan 03, 2024)
7-30504701-G-A			Likely benign (Jul 03, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GGCT	protein_coding	protein_coding	ENST00000275428	4	54859

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000143	0.669	125703	0	44	125747	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.294	91	99.3	0.917	0.00000453	1241
Missense in Polyphen		31	32.208	0.9625		377
Synonymous	-0.369	40	37.1	1.08	0.00000190	347
Loss of Function	0.834	7	9.82	0.713	4.86e-7	108

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000267	0.000264
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000883	0.0000879
Middle Eastern	0.000272	0.000272
South Asian	0.000717	0.000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the formation of 5-oxoproline from gamma- glutamyl dipeptides and may play a significant role in glutathione homeostasis. Induces release of cytochrome c from mitochondria with resultant induction of apoptosis. {ECO:0000269|PubMed:16765912, ECO:0000269|PubMed:18515354}.
• Pathway: Glutathione metabolism - Homo sapiens (human);Gamma-glutamyl-transpeptidase deficiency;5-oxoprolinase deficiency;Gamma-Glutamyltransferase Deficiency;Glutathione Metabolism;Glutathione Synthetase Deficiency;5-Oxoprolinuria;Glutathione conjugation;Phase II - Conjugation of compounds;Biological oxidations;Metabolism;γ-glutamyl cycle;Glutathione synthesis and recycling (Consensus)

Recessive Scores

• pRec: 0.147

Intolerance Scores

• loftool: 0.551
• rvis_EVS: 0.1
• rvis_percentile_EVS: 61.28

Haploinsufficiency Scores

• pHI: 0.113
• hipred: N
• hipred_score: 0.394
• ghis: 0.462

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.283

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ggct

Gene ontology

• Biological process: release of cytochrome c from mitochondria;glutathione biosynthetic process
• Cellular component: cytosol;extracellular exosome
• Molecular function: gamma-glutamylcyclotransferase activity;protein homodimerization activity