GLOD5

glyoxalase domain containing 5, the group of Glyoxalase domain containing family

Basic information

Region (hg38): X:48761746-48773648

Links

ENSG00000171433 ∙ NCBI:392465 ∙ ∙ HGNC:33358 ∙ Uniprot:A6NK44 ∙ 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 GLOD5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GLOD5 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				1		1
missense			6	3		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	4	0

Variants in GLOD5

This is a list of pathogenic ClinVar variants found in the GLOD5 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-48761797-C-T		not specified	Likely benign (Mar 01, 2023)
X-48765841-A-G		not specified	Uncertain significance (Jul 20, 2021)
X-48765878-G-A		not specified	Likely benign (Nov 09, 2021)
X-48765898-A-G		not specified	Uncertain significance (Mar 28, 2023)
X-48765902-C-T		not specified	Uncertain significance (Dec 03, 2021)
X-48765961-A-G		not specified	Likely benign (Dec 01, 2022)
X-48770948-T-G		not specified	Uncertain significance (Mar 21, 2023)
X-48771050-G-A		not specified	Uncertain significance (Dec 20, 2023)
X-48773386-G-A		not specified	Uncertain significance (Aug 28, 2023)
X-48773393-C-T			Likely benign (Mar 01, 2022)
X-48773431-C-T		not specified	Uncertain significance (Mar 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GLOD5	protein_coding	protein_coding	ENST00000303227	4	11911

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0533	0.715	124579	0	3	124582	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.610	70	57.0	1.23	0.00000436	1049
Missense in Polyphen		25	18.873	1.3246		350
Synonymous	0.198	21	22.2	0.946	0.00000182	306
Loss of Function	0.715	2	3.43	0.583	2.16e-7	79

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000157	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.0000131	0.00000885
Middle Eastern	0.000157	0.000111
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.520
• rvis_EVS: 0.84
• rvis_percentile_EVS: 88.18

Haploinsufficiency Scores

• pHI: 0.199
• hipred: N
• hipred_score: 0.220
• ghis: 0.395

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: 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

Mouse Genome Informatics

• Gene name: Glod5
• Phenotype: normal phenotype