GGTLC2

gamma-glutamyltransferase light chain 2, the group of Gamma-glutamyltransferases

Basic information

Region (hg38): 22:22644614-22647898

Previous symbols: [ "GGTL4" ]

Links

ENSG00000100121 ∙ NCBI:91227 ∙ OMIM:612339 ∙ HGNC:18596 ∙ Uniprot:Q14390 ∙ 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 GGTLC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GGTLC2 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			38	1		39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	38	1	0

Variants in GGTLC2

This is a list of pathogenic ClinVar variants found in the GGTLC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-22646353-C-T		not specified	Uncertain significance (Jul 26, 2021)
22-22646391-G-C		not specified	Uncertain significance (Nov 14, 2023)
22-22646407-C-G		not specified	Uncertain significance (Oct 30, 2024)
22-22646437-C-T		not specified	Uncertain significance (Sep 04, 2024)
22-22646448-G-T			Likely benign (Dec 01, 2022)
22-22646472-G-A		not specified	Uncertain significance (Nov 22, 2024)
22-22646503-C-T		not specified	Uncertain significance (Mar 07, 2025)
22-22646525-G-A			Likely benign (Jan 01, 2024)
22-22646770-C-T		not specified	Uncertain significance (Jun 12, 2023)
22-22646774-C-A		not specified	Uncertain significance (Jun 30, 2022)
22-22646782-A-G		not specified	Uncertain significance (Jan 16, 2024)
22-22646828-A-G		not specified	Uncertain significance (Aug 13, 2021)
22-22646839-G-A		not specified	Uncertain significance (Jan 19, 2024)
22-22646867-A-G		not specified	Uncertain significance (Apr 12, 2023)
22-22646992-C-G		not specified	Uncertain significance (Jan 24, 2024)
22-22646992-C-T		not specified	Uncertain significance (May 02, 2024)
22-22646998-C-G		not specified	Uncertain significance (Jul 19, 2022)
22-22646998-C-T		not specified	Uncertain significance (Jan 26, 2023)
22-22647013-C-A		not specified	Uncertain significance (Aug 12, 2021)
22-22647025-G-T		not specified	Uncertain significance (Jun 21, 2022)
22-22647033-G-A		not specified	Uncertain significance (Oct 04, 2024)
22-22647145-C-A		not specified	Uncertain significance (Nov 13, 2024)
22-22647148-G-C		not specified	Uncertain significance (Jan 30, 2024)
22-22647166-C-T		not specified	Uncertain significance (Sep 30, 2024)
22-22647169-T-C		not specified	Uncertain significance (Jan 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GGTLC2	protein_coding	protein_coding	ENST00000480559	5	1589

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000232	0.310	125524	0	36	125560	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.646	145	125	1.16	0.00000814	1382
Missense in Polyphen		40	37.763	1.0592		476
Synonymous	-1.90	76	57.7	1.32	0.00000456	435
Loss of Function	0.00519	7	7.01	0.998	3.00e-7	86

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000276	0.000243
Ashkenazi Jewish	0.000105	0.0000993
East Asian	0.000456	0.000435
Finnish	0.000470	0.000462
European (Non-Finnish)	0.0000715	0.0000705
Middle Eastern	0.000456	0.000435
South Asian	0.0000980	0.0000980
Other	0.000167	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Prostaglandin Leukotriene metabolism (Consensus)

Haploinsufficiency Scores

• pHI: 0.171
• hipred: N
• hipred_score: 0.187

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Gene ontology

• Biological process: proteolysis;glutathione catabolic process;biological_process;leukotriene D4 biosynthetic process
• Cellular component: extracellular exosome
• Molecular function: molecular_function;glutathione hydrolase activity