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

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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.

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				3	4	7
missense			37	1	1	39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	4	5

Variants in MGAT1

This is a list of pathogenic ClinVar variants found in the MGAT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-180791665-G-A		not specified	Uncertain significance (Aug 15, 2024)
5-180791673-G-A			Likely benign (Aug 17, 2018)
5-180791693-G-A		not specified	Uncertain significance (Jan 07, 2022)
5-180791699-G-A		not specified	Uncertain significance (Mar 18, 2024)
5-180791709-G-A			Benign (Apr 26, 2018)
5-180791717-T-C		not specified	Uncertain significance (Nov 12, 2021)
5-180791720-C-A		not specified	Uncertain significance (Mar 30, 2024)
5-180791731-G-C		not specified	Uncertain significance (Aug 14, 2023)
5-180791746-G-A		not specified	Uncertain significance (Jan 12, 2024)
5-180791817-C-T			Likely benign (May 15, 2018)
5-180791818-C-T		not specified	Uncertain significance (Jan 08, 2024)
5-180791839-C-T		not specified	Uncertain significance (Jun 05, 2023)
5-180791840-G-A		not specified	Uncertain significance (Aug 14, 2024)
5-180791863-A-C		not specified	Uncertain significance (Aug 17, 2021)
5-180791866-T-C		not specified	Uncertain significance (May 05, 2023)
5-180791891-G-A		not specified	Uncertain significance (Mar 30, 2024)
5-180791897-G-A		not specified	Uncertain significance (Apr 26, 2023)
5-180791962-T-C		not specified	Uncertain significance (Dec 03, 2021)
5-180791983-T-C		not specified	Uncertain significance (Nov 11, 2024)
5-180792009-G-T		not specified	Uncertain significance (May 31, 2024)
5-180792016-A-G		not specified	Uncertain significance (Jun 27, 2022)
5-180792119-T-G		not specified	Uncertain significance (Mar 06, 2023)
5-180792130-G-C		not specified	Uncertain significance (Mar 06, 2023)
5-180792242-T-G		not specified	Uncertain significance (Oct 01, 2024)
5-180792256-G-A		not specified	Uncertain significance (Feb 12, 2024)

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
0.989	0.0112	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

Haploinsufficiency Scores

• pHI: 0.251
• hipred: Y
• hipred_score: 0.572
• ghis: 0.457

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

Mouse Genome Informatics

• Gene name: Mgat1
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; reproductive 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); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); growth/size/body region phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; embryo phenotype

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