MGAT1

protein-coding

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

Gene summary

There are believed to be over 100 different glycosyltransferases involved in the synthesis of protein-bound and lipid-bound oligosaccharides. UDP-N-acetylglucosamine:alpha-3-D-mannoside beta-1,2-N-acetylglucosaminyltransferase I is a medial-Golgi enzyme essential for the synthesis of hybrid and complex N-glycans. The protein, encoded by a single exon, shows typical features of a type II transmembrane protein. The protein is believed to be essential for normal embryogenesis. Several variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

Previous symbols:

MGAT
GLYT1

MANE transcript

NM_002406.4

Inheritance

—

ClinVar variants

U:71B:11

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr5:180,784,780-180,815,652

External References & Databases

Ensembl (ENSG00000131446)

Transcript & Mutation Effects

hg38 • Region Span ~30.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MGAT1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 72

not providedTotal: 8

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002406.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	4 clinvar	4 clinvar	9
missense			70 clinvar	2 clinvar	1 clinvar	73
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	71	6	5	82

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 121 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002406.4	RefSeq	NP_002397.2	1	MANE Select
ENST00000307826.5	Ensembl	ENSP00000311888.4	1	MANE Select
NM_001114617.2	RefSeq	NP_001108089.1	1	Standard
NM_001114618.1	RefSeq	NP_001108090.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

in utero embryonic development
UDP-N-acetylglucosamine catabolic process
protein glycosylation
protein N-linked glycosylation
protein N-linked glycosylation via asparagine

Molecular Function

alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity
acetylglucosaminyltransferase activity
manganese ion binding

Cellular Component

Golgi membrane
Golgi apparatus
membrane
integral component of membrane
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000446023
Coding exons: 1
Length: 25112
Individuals with no LoFs: 125696
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 125700
p: 0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.51	230	304	0.756	0.0000222	2823
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0	0.0	absent
Finnish	0.000048	0.000046	rare
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Initiates complex N-linked carbohydrate formation. Essential for the conversion of high-mannose to hybrid and complex N-glycans.;

Recessive Scores

pRec: 0.136

Intolerance Scores

LoFtool: 0.00172
RVIS EVS: 0.2
RVIS percentile EVS: 67.3

Essentials

Essential (CRISPR): E
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.514

Gene Damage Prediction

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