GLOD4

glyoxalase domain containing 4, the group of Glyoxalase domain containing family

Basic information

Region (hg38): 17:757097-782294

Previous symbols: [ "C17orf25" ]

Links

ENSG00000167699 ∙ NCBI:51031 ∙ ∙ HGNC:14111 ∙ Uniprot:Q9HC38 ∙ 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 GLOD4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GLOD4 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			27	1		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	1	0

Variants in GLOD4

This is a list of pathogenic ClinVar variants found in the GLOD4 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-760183-G-A		not specified	Uncertain significance (Aug 20, 2024)
17-760235-T-C		not specified	Uncertain significance (Aug 08, 2023)
17-769886-T-C		not specified	Uncertain significance (Sep 07, 2022)
17-769895-G-T		not specified	Uncertain significance (Aug 12, 2021)
17-769898-C-A		not specified	Uncertain significance (Mar 17, 2023)
17-769911-T-A		not specified	Uncertain significance (Aug 19, 2024)
17-769928-C-A		not specified	Uncertain significance (Nov 22, 2024)
17-769940-A-C		not specified	Uncertain significance (Jun 10, 2024)
17-770131-T-G		not specified	Uncertain significance (Dec 10, 2024)
17-770453-C-G		not specified	Uncertain significance (Sep 27, 2022)
17-770474-C-G		not specified	Uncertain significance (Oct 29, 2024)
17-771335-G-A		not specified	Uncertain significance (Mar 20, 2023)
17-771368-T-C		not specified	Uncertain significance (Nov 24, 2024)
17-771386-A-T		not specified	Uncertain significance (Jan 31, 2024)
17-771451-T-G		not specified	Uncertain significance (May 25, 2022)
17-771456-C-G		not specified	Uncertain significance (Jul 06, 2021)
17-775777-G-A		not specified	Uncertain significance (Nov 12, 2024)
17-775786-A-G		not specified	Likely benign (Feb 03, 2022)
17-775875-C-G		not specified	Uncertain significance (Jun 29, 2023)
17-775892-C-A		not specified	Uncertain significance (Aug 28, 2024)
17-775912-G-A		not specified	Uncertain significance (Nov 09, 2024)
17-776900-C-A		not specified	Uncertain significance (Apr 20, 2024)
17-776924-C-T		not specified	Uncertain significance (Apr 27, 2023)
17-776954-C-G		not specified	Uncertain significance (Nov 13, 2023)
17-782180-C-A		not specified	Uncertain significance (Mar 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GLOD4	protein_coding	protein_coding	ENST00000301329	9	25245

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.07e-13	0.0165	125692	0	56	125748	0.000223

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.00840	168	168	0.998	0.00000876	1958
Missense in Polyphen		62	64.361	0.96332		749
Synonymous	-0.685	73	65.9	1.11	0.00000392	551
Loss of Function	-0.302	18	16.7	1.08	7.69e-7	208

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000820	0.000820
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000217	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000238	0.000237
Middle Eastern	0.000217	0.000217
South Asian	0.000197	0.000196
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Glycine, serine, alanine and threonine metabolism (Consensus)

Recessive Scores

• pRec: 0.0866

Intolerance Scores

• loftool: 0.812
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.77

Haploinsufficiency Scores

• pHI: 0.104
• hipred: N
• hipred_score: 0.255
• ghis: 0.578

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.496

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Glod4

Gene ontology

• Cellular component: mitochondrion;extracellular exosome
• Molecular function: cadherin binding