GLCE

glucuronic acid epimerase

Basic information

Region (hg38): 15:69160583-69272217

Links

ENSG00000138604 ∙ NCBI:26035 ∙ OMIM:612134 ∙ HGNC:17855 ∙ Uniprot:O94923 ∙ 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 GLCE gene.

• Inborn genetic diseases (14 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GLCE 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			12	1	1	14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	13	1	2

Variants in GLCE

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

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

Position	Type	Phenotype	Significance	ClinVar
15-69255858-G-A		not specified	Uncertain significance (Sep 14, 2022)
15-69255910-A-G		not specified	Uncertain significance (Jun 05, 2023)
15-69255920-G-T		not specified	Uncertain significance (Feb 17, 2022)
15-69255927-C-T		not specified	Uncertain significance (Apr 18, 2023)
15-69255964-A-C		not specified	Uncertain significance (Jan 18, 2022)
15-69256008-G-A		not specified	Likely benign (Mar 27, 2023)
15-69256054-A-G			Benign (Jul 16, 2018)
15-69256245-G-A		not specified	Uncertain significance (Jan 04, 2024)
15-69261171-A-G		not specified	Uncertain significance (Dec 02, 2021)
15-69261260-A-C		not specified	Uncertain significance (Dec 12, 2023)
15-69268421-G-T		not specified	Uncertain significance (Sep 22, 2023)
15-69268493-A-T		not specified	Uncertain significance (Apr 25, 2022)
15-69268521-C-G			Benign (Jul 16, 2018)
15-69268580-C-G		not specified	Uncertain significance (Mar 17, 2023)
15-69268738-G-A		not specified	Uncertain significance (Jan 18, 2022)
15-69268747-A-G		not specified	Uncertain significance (Jan 10, 2023)
15-69268748-C-T		not specified	Uncertain significance (Aug 04, 2023)
15-69268841-A-G		not specified	Uncertain significance (Feb 28, 2023)
15-69268939-A-C		not specified	Uncertain significance (Apr 11, 2023)
15-69269057-C-T		not specified	Uncertain significance (Jan 30, 2024)
15-69269225-G-A		not specified	Uncertain significance (Apr 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GLCE	protein_coding	protein_coding	ENST00000261858	3	111634

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.654	0.346	125722	0	25	125747	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.71	242	329	0.735	0.0000168	4076
Missense in Polyphen		55	120.24	0.45744		1415
Synonymous	0.708	110	120	0.918	0.00000594	1182
Loss of Function	3.43	4	20.9	0.191	0.00000107	279

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.000416	0.000416
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Converts D-glucuronic acid residues adjacent to N- sulfate sugar residues to L-iduronic acid residues, both in maturing heparan sulfate (HS) and heparin chains. This is important for further modifications that determine the specificity of interactions between these glycosaminoglycans and proteins. {ECO:0000269|PubMed:20118238}.
• Pathway: Glycosaminoglycan biosynthesis - heparan sulfate / heparin - Homo sapiens (human);Metabolism of carbohydrates;HS-GAG biosynthesis;Heparan sulfate/heparin (HS-GAG) metabolism;Glycosaminoglycan metabolism;heparan sulfate biosynthesis (late stages);heparan sulfate biosynthesis;Metabolism (Consensus)

Recessive Scores

• pRec: 0.234

Intolerance Scores

• loftool: 0.547
• rvis_EVS: 0.09
• rvis_percentile_EVS: 60.47

Haploinsufficiency Scores

• pHI: 0.327
• hipred: Y
• hipred_score: 0.626
• ghis: 0.548

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: N
• gene_indispensability_score: 0.111

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Glce
• Phenotype: respiratory system 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); limbs/digits/tail phenotype; digestive/alimentary phenotype; vision/eye phenotype; skeleton phenotype; renal/urinary system phenotype; growth/size/body region phenotype; craniofacial phenotype

Gene ontology

• Biological process: heparan sulfate proteoglycan biosynthetic process;heparin biosynthetic process
• Cellular component: Golgi membrane;Golgi apparatus;integral component of membrane
• Molecular function: racemase and epimerase activity, acting on carbohydrates and derivatives;heparosan-N-sulfate-glucuronate 5-epimerase activity