GCLM
glutamate-cysteine ligase modifier subunit
Basic information
Region (hg38): 1:93885198-93909456
Previous symbols: [ "GLCLR" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the GCLM 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 | 2 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region ? | 0 | |||||
| non coding ? | 0 | |||||
| Total | 0 | 0 | 2 | 0 | 0 |
Variants in GCLM
This is a list of pathogenic ClinVar variants found in the GCLM region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-93889067-A-C | Uncertain significance (-) | |||
| 1-93896737-C-G | not specified | Uncertain significance (Oct 06, 2021) | ||
| 1-93896752-C-G | not specified | Uncertain significance (Dec 07, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| GCLM | protein_coding | protein_coding | ENST00000370238 | 7 | 24206 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.990 | 0.00989 | 125741 | 0 | 4 | 125745 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.36 | 82 | 125 | 0.658 | 0.00000573 | 1768 |
| Missense in Polyphen | 19 | 37.422 | 0.50773 | 527 | ||
| Synonymous | 1.19 | 36 | 46.3 | 0.778 | 0.00000229 | 514 |
| Loss of Function | 3.45 | 0 | 13.9 | 0.00 | 5.92e-7 | 178 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000356 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Pathway
- Glutathione metabolism - Homo sapiens (human);Cysteine and methionine metabolism - Homo sapiens (human);Ferroptosis - Homo sapiens (human);Beta-mercaptolactate-cysteine disulfiduria;2-Hydroxyglutric Aciduria (D And L Form);Gamma-glutamyl-transpeptidase deficiency;5-oxoprolinase deficiency;Gamma-Glutamyltransferase Deficiency;Glutathione Metabolism;Cysteine Metabolism;Homocarnosinosis;Hyperinsulinism-Hyperammonemia Syndrome;Glutathione Synthetase Deficiency;Succinic semialdehyde dehydrogenase deficiency;Cystinosis, ocular nonnephropathic;4-Hydroxybutyric Aciduria/Succinic Semialdehyde Dehydrogenase Deficiency;5-Oxoprolinuria;Glutamate Metabolism;Glutathione metabolism;Trans-sulfuration pathway;Trans-sulfuration and one carbon metabolism;Nuclear Receptors Meta-Pathway;NRF2 pathway;Transcriptional activation by NRF2;Photodynamic therapy-induced NFE2L2 (NRF2) survival signaling;Amino Acid metabolism;One carbon metabolism and related pathways;Glutathione conjugation;Phase II - Conjugation of compounds;Glutamate Glutamine metabolism;Biological oxidations;Metabolism;glutathione biosynthesis;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;Arginine Proline metabolism;γ-glutamyl cycle;Glutathione synthesis and recycling
(Consensus)
Recessive Scores
- pRec
- 0.348
Intolerance Scores
- loftool
- 0.414
- rvis_EVS
- -0.16
- rvis_percentile_EVS
- 41.25
Haploinsufficiency Scores
- pHI
- 0.199
- hipred
- Y
- hipred_score
- 0.654
- ghis
- 0.504
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.941
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Gclm
- Phenotype
- homeostasis/metabolism phenotype; cellular phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);
Gene ontology
- Biological process
- cysteine metabolic process;glutamate metabolic process;glutathione biosynthetic process;response to oxidative stress;aging;response to nutrient;apoptotic mitochondrial changes;response to activity;positive regulation of glutamate-cysteine ligase activity;cellular response to hepatocyte growth factor stimulus;hepatic stellate cell activation;response to drug;negative regulation of neuron apoptotic process;cellular response to fibroblast growth factor stimulus;response to human chorionic gonadotropin;regulation of blood vessel size;response to nitrosative stress;regulation of mitochondrial depolarization;cellular response to glucose stimulus;cellular response to follicle-stimulating hormone stimulus;cellular response to thyroxine stimulus;cellular response to leukemia inhibitory factor;negative regulation of extrinsic apoptotic signaling pathway
- Cellular component
- cytosol;glutamate-cysteine ligase complex
- Molecular function
- glutamate-cysteine ligase activity;enzyme regulator activity;glutamate-cysteine ligase catalytic subunit binding;protein heterodimerization activity