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.

• not_specified (59 variants)
• not_provided (3 variants)

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. These statistics are base on transcript: NM_000012215.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			58	1		59
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	58	1	0

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