OGA

O-GlcNAcase, the group of Hexosaminidases

Basic information

Region (hg38): 10:101784443-101818465

Previous symbols: [ "MGEA5" ]

Links

ENSG00000198408 ∙ NCBI:10724 ∙ OMIM:604039 ∙ HGNC:7056 ∙ Uniprot:O60502 ∙ 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 OGA gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OGA 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			38			38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	1	3
non coding						0
Total	0	0	38	0	0

Variants in OGA

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

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

Position	Type	Phenotype	Significance	ClinVar
10-101786507-T-C		not specified	Uncertain significance (Dec 23, 2024)
10-101786582-G-A		not specified	Uncertain significance (Dec 22, 2023)
10-101787465-T-C		not specified	Uncertain significance (Apr 18, 2023)
10-101792865-T-G		not specified	Uncertain significance (Dec 01, 2022)
10-101792874-C-T		not specified	Uncertain significance (Aug 16, 2021)
10-101792876-T-C		not specified	Uncertain significance (Feb 02, 2024)
10-101798058-T-C		not specified	Uncertain significance (Sep 26, 2024)
10-101798141-C-T		not specified	Uncertain significance (Dec 03, 2024)
10-101798974-C-A		not specified	Uncertain significance (Jan 21, 2025)
10-101798984-T-C		not specified	Uncertain significance (Oct 07, 2024)
10-101798988-G-C		not specified	Uncertain significance (Jul 14, 2021)
10-101799006-T-C		not specified	Uncertain significance (Jul 07, 2024)
10-101799051-T-C		not specified	Uncertain significance (Jan 10, 2025)
10-101799075-G-C		not specified	Uncertain significance (Jan 24, 2023)
10-101799135-T-G		not specified	Uncertain significance (Aug 22, 2023)
10-101799182-G-A		not specified	Uncertain significance (Feb 08, 2025)
10-101799224-T-A		not specified	Uncertain significance (Dec 17, 2023)
10-101799261-G-A		not specified	Uncertain significance (Apr 22, 2024)
10-101799300-G-C		not specified	Uncertain significance (Feb 28, 2024)
10-101799300-G-T		not specified	Uncertain significance (Aug 17, 2021)
10-101799306-T-G		not specified	Uncertain significance (Mar 02, 2023)
10-101799369-C-T		not specified	Uncertain significance (May 04, 2023)
10-101800244-C-T		not specified	Uncertain significance (Jun 03, 2024)
10-101800346-C-G		not specified	Uncertain significance (Nov 19, 2024)
10-101800403-G-A			Likely benign (Jun 08, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OGA	protein_coding	protein_coding	ENST00000361464	16	34497

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.966	0.0343	125735	0	12	125747	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.00	297	482	0.616	0.0000237	6045
Missense in Polyphen		57	175.84	0.32415		2294
Synonymous	-0.379	173	167	1.04	0.00000825	1702
Loss of Function	5.17	8	45.7	0.175	0.00000229	576

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000216	0.000216
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Isoform 1: Cleaves GlcNAc but not GalNAc from O- glycosylated proteins. Can use p-nitrophenyl-beta-GlcNAc and 4- methylumbelliferone-GlcNAc as substrates but not p-nitrophenyl- beta-GalNAc or p-nitrophenyl-alpha-GlcNAc (in vitro) (PubMed:11148210). Does not bind acetyl-CoA and does not have histone acetyltransferase activity (PubMed:24088714). {ECO:0000269|PubMed:11148210, ECO:0000269|PubMed:11788610, ECO:0000269|PubMed:20673219, ECO:0000269|PubMed:22365600, ECO:0000269|PubMed:24088714}.

Recessive Scores

• pRec: 0.210

Intolerance Scores

• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.73

Haploinsufficiency Scores

• pHI: 0.667
• hipred: Y
• hipred_score: 0.756
• ghis: 0.558

Essentials

• essential_gene_gene_trap: E

Mouse Genome Informatics

• Gene name: Mgea5
• 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); cellular phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: N-acetylglucosamine metabolic process;protein O-linked glycosylation;glycoprotein catabolic process;protein deglycosylation;glycoprotein metabolic process;viral process
• Cellular component: nucleus;cytosol;membrane
• Molecular function: hyalurononglucosaminidase activity;beta-N-acetylglucosaminidase activity;[protein]-3-O-(N-acetyl-D-glucosaminyl)-L-threonine O-N-acetyl-alpha-D-glucosaminase activity;[protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine O-N-acetyl-alpha-D-glucosaminase activity;[protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity