GGTLC1

gamma-glutamyltransferase light chain 1, the group of Gamma-glutamyltransferases

Basic information

Region (hg38): 20:23985049-23988779

Previous symbols: [ "GGTLA4", "GGTLA3" ]

Links

ENSG00000149435 ∙ NCBI:92086 ∙ OMIM:612338 ∙ HGNC:16437 ∙ Uniprot:Q9BX51 ∙ 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 GGTLC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GGTLC1 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			16		1	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	0	1

Variants in GGTLC1

This is a list of pathogenic ClinVar variants found in the GGTLC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-23985233-C-T		not specified	Uncertain significance (Mar 29, 2023)
20-23985310-G-T		not specified	Uncertain significance (Feb 05, 2024)
20-23985338-G-A		not specified	Uncertain significance (May 30, 2024)
20-23985723-G-A		not specified	Uncertain significance (Feb 15, 2023)
20-23985747-C-T		not specified	Uncertain significance (Aug 16, 2021)
20-23985887-G-A		not specified	Uncertain significance (Aug 17, 2022)
20-23985944-G-A		not specified	Uncertain significance (Nov 18, 2022)
20-23985954-T-A			Benign (Dec 11, 2017)
20-23985959-G-A		not specified	Uncertain significance (Dec 06, 2023)
20-23985960-A-G		not specified	Uncertain significance (May 09, 2023)
20-23986094-C-G		not specified	Uncertain significance (Dec 01, 2023)
20-23986105-G-A		not specified	Uncertain significance (Jan 10, 2023)
20-23986132-G-T		not specified	Uncertain significance (Aug 22, 2023)
20-23986149-C-T		not specified	Uncertain significance (Sep 01, 2021)
20-23986458-C-A		not specified	Uncertain significance (Jan 08, 2024)
20-23986458-C-T		not specified	Uncertain significance (May 18, 2022)
20-23986509-C-T		not specified	Uncertain significance (Jan 04, 2022)
20-23986518-G-A		not specified	Uncertain significance (Mar 23, 2022)
20-23986523-T-C		not specified	Uncertain significance (Apr 06, 2024)
20-23986563-C-T		not specified	Uncertain significance (May 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GGTLC1	protein_coding	protein_coding	ENST00000335694	5	3727

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000334	0.370	125455	0	136	125591	0.000542

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.18	179	140	1.28	0.00000967	1467
Missense in Polyphen		55	40.074	1.3725		476
Synonymous	-0.680	66	59.3	1.11	0.00000501	458
Loss of Function	0.174	7	7.51	0.932	3.29e-7	86

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000738	0.000738
Ashkenazi Jewish	0.00	0.00
East Asian	0.000381	0.000381
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000812	0.000811
Middle Eastern	0.000381	0.000381
South Asian	0.000294	0.000294
Other	0.000653	0.000653

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.872
• rvis_EVS: 0.89
• rvis_percentile_EVS: 89.14

Haploinsufficiency Scores

• pHI: 0.206
• hipred: N
• hipred_score: 0.112

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: cellular_component
• Molecular function: molecular_function;glutathione hydrolase activity