MGAT1

alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase, the group of Mannosyl-glycoprotein N-acetylglucosaminyltransferases

Basic information

Region (hg38): 5:180784780-180815652

Previous symbols: [ "MGAT", "GLYT1" ]

Links

ENSG00000131446 ∙ NCBI:4245 ∙ OMIM:160995 ∙ HGNC:7044 ∙ Uniprot:P26572 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 81.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
ENST00000307826.5	ENSP00000311888.4	1	yes	-
ENST00000333055.8	ENSP00000332073.3	1	-	-
ENST00000393340.7	ENSP00000377010.3	1	-	-
ENST00000427865.2	ENSP00000402838.2	1	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MGAT1 gene.

• not_specified (71 variants)
• not_provided (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MGAT1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002406.4. 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			1	4	4	9
missense			69	2	1	72
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	70	6	5

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MGAT1	protein_coding	protein_coding	ENST00000446023	1	25112

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125696	0	4	125700	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.51	230	304	0.756	0.0000222	2823
Missense in Polyphen		41	115.09	0.35623		1116
Synonymous	-1.53	164	141	1.16	0.0000106	957
Loss of Function	3.41	0	13.5	0.00	6.71e-7	127

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.0000477	0.0000462
European (Non-Finnish)	0.00000881	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Initiates complex N-linked carbohydrate formation. Essential for the conversion of high-mannose to hybrid and complex N-glycans.
• Pathway: N-Glycan biosynthesis - Homo sapiens (human);Post-translational protein modification;Metabolism of proteins;N-glycan trimming and elongation in the cis-Golgi;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;N-Glycan biosynthesis (Consensus)

Recessive Scores

• pRec: 0.136

Intolerance Scores

• loftool: 0.00172
• rvis_EVS: 0.2
• rvis_percentile_EVS: 67.3

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.514

Gene Damage Prediction

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

Gene ontology

• Biological process: in utero embryonic development;UDP-N-acetylglucosamine catabolic process;protein glycosylation;protein N-linked glycosylation;protein N-linked glycosylation via asparagine
• Cellular component: Golgi membrane;Golgi apparatus;membrane;integral component of membrane;extracellular exosome;extracellular vesicle
• Molecular function: alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity;acetylglucosaminyltransferase activity;manganese ion binding