GGTLC2

protein-coding

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

Gene summary

This gene encodes a protein related to enzymes that cleaves gamma-glutamyl peptide bonds in glutathione and other peptides. Unlike similar proteins, the encoded protein contains only the light chain portion and may not have catalytic activity. Alternative splicing results in multiple transcript variants. There are several related family members and related pseudogene for this gene situated in the same region of chromosome 22. [provided by RefSeq, Sep 2013]

Previous symbols:

GGTL4

MANE transcript

NM_199127.3

Inheritance

—

ClinVar variants

U:67B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1

Max pathogenic AF

—

Genomic locus

chr22:22,644,614-22,647,898

External References & Databases

Ensembl (ENSG00000100121)

Transcript & Mutation Effects

hg38 • Region Span ~3.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GGTLC2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 67

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_199127.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			67 clinvar	1 clinvar		68
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	67	1	0	68

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 14 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_199127.3	RefSeq	NP_954578.2	5	MANE Select
ENST00000448514.3	Ensembl	ENSP00000415676.2	5	MANE Select
NM_001282879.2	RefSeq	NP_001269808.1	4	Standard
NM_001391910.1	RefSeq	NP_001378839.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Prostaglandin Leukotriene metabolism

Biological Process

proteolysis
glutathione catabolic process
biological_process
leukotriene D4 biosynthetic process

Molecular Function

molecular_function
glutathione hydrolase activity

Cellular Component

extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000480559
Coding exons: 5
Length: 1589
Individuals with no LoFs: 125524
Homozygous LoFs: 0
Heterozygous LoFs: 36
Defined: 125560
p: 0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.646	145	125	1.16	0.00000814	1382
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00022	0.00018	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.00011	0.000099	rare
East Asian	0.00046	0.00044	rare
Finnish	0.00047	0.00046	rare
European (Non-Finnish)	0.000071	0.000071	rare
South Asian	0.000098	0.000098	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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