GLO1

glyoxalase I, the group of Glyoxalase domain containing family

Basic information

Region (hg38): 6:38675924-38703145

Links

ENSG00000124767 ∙ NCBI:2739 ∙ OMIM:138750 ∙ HGNC:4323 ∙ Uniprot:Q04760 ∙ 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 GLO1 gene.

• Inborn genetic diseases (9 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GLO1 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			9			9
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	9	0	0

Variants in GLO1

This is a list of pathogenic ClinVar variants found in the GLO1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-38677376-C-A		not specified	Uncertain significance (Aug 02, 2021)
6-38682074-A-C		not specified	Uncertain significance (Oct 26, 2022)
6-38682074-A-G		not specified	Uncertain significance (Jul 12, 2023)
6-38682106-C-T			Likely benign (Jul 19, 2018)
6-38682852-T-G		Autism, susceptibility to, 1	Uncertain significance (Dec 30, 2010)
6-38684499-A-C		not specified	Uncertain significance (Jun 18, 2021)
6-38702981-G-C		not specified	Uncertain significance (Feb 23, 2023)
6-38703013-C-A		not specified	Uncertain significance (Mar 29, 2022)
6-38703015-C-G		not specified	Uncertain significance (Aug 04, 2023)
6-38703015-C-T		not specified	Uncertain significance (Oct 03, 2022)
6-38703027-C-T		not specified	Uncertain significance (Nov 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GLO1	protein_coding	protein_coding	ENST00000373365	6	27217

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.67e-7	0.336	125648	0	99	125747	0.000394

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.420	82	93.4	0.878	0.00000438	1205
Missense in Polyphen		29	32.07	0.90426		411
Synonymous	-0.0825	34	33.4	1.02	0.00000156	322
Loss of Function	0.419	10	11.5	0.867	7.47e-7	126

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00205	0.00191
Ashkenazi Jewish	0.00	0.00
East Asian	0.00185	0.00169
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000226	0.000220
Middle Eastern	0.00185	0.00169
South Asian	0.000231	0.000229
Other	0.000333	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the conversion of hemimercaptal, formed from methylglyoxal and glutathione, to S-lactoylglutathione. Involved in the regulation of TNF-induced transcriptional activity of NF- kappa-B. Required for normal osteoclastogenesis. {ECO:0000269|PubMed:19199007, ECO:0000269|PubMed:23122816, ECO:0000269|PubMed:9705294}.
• Pathway: Pyruvate metabolism - Homo sapiens (human);Pyruvate Dehydrogenase Complex Deficiency;Primary hyperoxaluria II, PH2;Pyruvate kinase deficiency;Leigh Syndrome;Pyruvate Metabolism;Pyruvate Decarboxylase E1 Component Deficiency (PDHE1 Deficiency);Pyruvaldehyde Degradation;Pyruvate metabolism;Pyruvate metabolism and Citric Acid (TCA) cycle;The citric acid (TCA) cycle and respiratory electron transport;Metabolism;Pyruvate metabolism;methylglyoxal degradation I (Consensus)

Recessive Scores

• pRec: 0.906

Intolerance Scores

• loftool: 0.821
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.76

Haploinsufficiency Scores

• pHI: 0.350
• hipred: N
• hipred_score: 0.401
• ghis: 0.616

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.969

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Glo1
• Phenotype: homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: glo1
• Affected structure: blood vessel
• Phenotype tag: abnormal
• Phenotype quality: increased branchiness

Gene ontology

• Biological process: carbohydrate metabolic process;pyruvate metabolic process;regulation of transcription by RNA polymerase II;glutathione metabolic process;methylglyoxal metabolic process;osteoclast differentiation;negative regulation of apoptotic process
• Cellular component: nucleus;cytoplasm;cytosol;plasma membrane;extracellular exosome
• Molecular function: lactoylglutathione lyase activity;zinc ion binding