MGAT5

alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase, the group of MicroRNA protein coding host genes|Mannosyl-glycoprotein N-acetylglucosaminyltransferases

Basic information

Region (hg38): 2:134119982-134454621

Links

ENSG00000152127 ∙ NCBI:4249 ∙ OMIM:601774 ∙ HGNC:7049 ∙ Uniprot:Q09328 ∙ 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 MGAT5 gene.

• Inborn genetic diseases (13 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MGAT5 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				1		1
missense			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	1	0

Variants in MGAT5

This is a list of pathogenic ClinVar variants found in the MGAT5 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-134254410-C-T		not specified	Uncertain significance (Dec 03, 2021)
2-134254497-T-C		not specified	Uncertain significance (Sep 20, 2023)
2-134254543-G-A		not specified	Uncertain significance (Aug 17, 2021)
2-134270500-C-T		not specified	Uncertain significance (Mar 08, 2024)
2-134270505-A-G		not specified	Uncertain significance (Dec 20, 2022)
2-134270511-G-A		not specified	Uncertain significance (Sep 20, 2023)
2-134317564-C-T		not specified	Uncertain significance (Dec 14, 2021)
2-134338262-G-A		not specified	Uncertain significance (Nov 09, 2021)
2-134338268-C-T		not specified	Uncertain significance (Dec 17, 2023)
2-134338284-T-G		not specified	Uncertain significance (May 27, 2022)
2-134338340-C-T		not specified	Uncertain significance (Jul 25, 2023)
2-134338341-G-A		not specified	Uncertain significance (Jan 03, 2024)
2-134338362-T-C		not specified	Uncertain significance (Sep 22, 2022)
2-134338373-A-C		not specified	Uncertain significance (May 17, 2023)
2-134341632-A-C		not specified	Uncertain significance (May 09, 2023)
2-134341746-G-A		not specified	Uncertain significance (May 16, 2022)
2-134345054-G-C		not specified	Uncertain significance (Oct 25, 2022)
2-134403077-C-T			Likely benign (Aug 05, 2018)
2-134422823-C-T			Likely benign (Apr 01, 2024)
2-134448803-G-C		not specified	Uncertain significance (Oct 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MGAT5	protein_coding	protein_coding	ENST00000409645	16	334639

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000211	125738	0	9	125747	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.56	263	408	0.644	0.0000215	4924
Missense in Polyphen		48	126.79	0.37857		1606
Synonymous	-0.135	155	153	1.01	0.00000873	1364
Loss of Function	5.69	3	43.6	0.0689	0.00000236	475

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000463	0.0000462
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: Catalyzes the addition of N-acetylglucosamine in beta 1- 6 linkage to the alpha-linked mannose of biantennary N-linked oligosaccharides. It is one of the most important enzymes involved in the regulation of the biosynthesis of glycoprotein oligosaccharides.
• Pathway: N-Glycan biosynthesis - Homo sapiens (human);Post-translational protein modification;N-Glycan antennae elongation;N-glycan antennae elongation in the medial/trans-Golgi;Metabolism of proteins;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;N-Glycan biosynthesis (Consensus)

Recessive Scores

• pRec: 0.585

Intolerance Scores

• loftool: 0.00779
• rvis_EVS: -1.27
• rvis_percentile_EVS: 5.24

Haploinsufficiency Scores

• pHI: 0.101
• hipred: Y
• hipred_score: 0.768
• ghis: 0.578

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.645

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mgat5
• Phenotype: immune system phenotype; renal/urinary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; neoplasm; homeostasis/metabolism phenotype

Gene ontology

• Biological process: protein N-linked glycosylation;protein N-linked glycosylation via asparagine;positive regulation of cell migration;negative regulation of protein tyrosine phosphatase activity;positive regulation of STAT cascade
• Cellular component: Golgi membrane;Golgi apparatus;membrane;integral component of membrane;extracellular exosome
• Molecular function: protein phosphatase inhibitor activity;alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity;manganese ion binding