MGAT5B

alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase B, the group of Mannosyl-glycoprotein N-acetylglucosaminyltransferases

Basic information

Region (hg38): 17:76868404-76950393

Links

ENSG00000167889 ∙ NCBI:146664 ∙ OMIM:612441 ∙ HGNC:24140 ∙ Uniprot:Q3V5L5 ∙ 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 MGAT5B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MGAT5B 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		3
missense			40	2		42
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	5	0

Variants in MGAT5B

This is a list of pathogenic ClinVar variants found in the MGAT5B region.

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

Position	Type	Phenotype	Significance	ClinVar
17-76869063-G-C		not specified	Uncertain significance (Feb 28, 2024)
17-76872796-G-A		not specified	Uncertain significance (Dec 22, 2023)
17-76872805-C-T			Likely benign (Apr 01, 2023)
17-76872811-C-G		not specified	Uncertain significance (Mar 16, 2024)
17-76872841-C-T		not specified	Uncertain significance (Jun 11, 2024)
17-76872847-G-A		not specified	Uncertain significance (Apr 01, 2024)
17-76872864-G-A		not specified	Uncertain significance (Oct 05, 2022)
17-76872925-G-A		not specified	Uncertain significance (May 09, 2024)
17-76882172-G-A		not specified	Uncertain significance (Feb 14, 2024)
17-76882174-G-A		not specified	Uncertain significance (Sep 25, 2023)
17-76882193-G-A		not specified	Uncertain significance (Aug 04, 2023)
17-76882219-C-T		not specified	Uncertain significance (Aug 30, 2021)
17-76882220-G-A		not specified	Uncertain significance (Aug 08, 2023)
17-76882229-C-T		not specified	Uncertain significance (Jun 29, 2022)
17-76882265-G-A		not specified	Uncertain significance (Dec 19, 2022)
17-76882273-G-A		not specified	Uncertain significance (Dec 16, 2023)
17-76882283-A-G		not specified	Uncertain significance (May 26, 2023)
17-76902559-C-G		not specified	Uncertain significance (Aug 02, 2023)
17-76902584-G-A		not specified	Uncertain significance (Mar 01, 2024)
17-76902607-G-A		not specified	Uncertain significance (Jan 23, 2024)
17-76902643-C-T		not specified	Uncertain significance (Jan 26, 2022)
17-76903333-C-A		not specified	Uncertain significance (May 12, 2024)
17-76903353-C-T		not specified	Uncertain significance (Mar 01, 2023)
17-76904364-T-C		not specified	Uncertain significance (May 25, 2022)
17-76905215-G-A		not specified	Uncertain significance (Jun 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MGAT5B	protein_coding	protein_coding	ENST00000428789	16	81938

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0146	0.985	125726	0	21	125747	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.78	410	525	0.781	0.0000353	5196
Missense in Polyphen		133	221.29	0.60103		2102
Synonymous	-0.221	233	229	1.02	0.0000166	1580
Loss of Function	4.13	11	38.8	0.284	0.00000189	418

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000180	0.000178
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.00	0.00
Finnish	0.0000966	0.0000924
European (Non-Finnish)	0.0000813	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Glycosyltransferase that acts on alpha-linked mannose of N-glycans and O-mannosyl glycans. Catalyzes the transfer of N- acetylglucosamine (GlcNAc) to the beta 1-6 linkage of the mannose residue of GlcNAcbeta1,2-Manalpha on both the alpha1,3- and alpha1,6-linked mannose arms in the core structure of N-glycan. Also acts on the GlcNAcbeta1,2-Manalpha1-Ser/Thr moiety, forming a 2,6-branched structure in brain O-mannosyl glycan. Plays an active role in modulating integrin and laminin-dependent adhesion and migration of neuronal cells via its activity in the O-mannosyl glycan pathway. {ECO:0000269|PubMed:12941944, ECO:0000269|PubMed:14617637, ECO:0000269|PubMed:14623122, ECO:0000269|PubMed:16606368, ECO:0000269|PubMed:16857188}.
• Pathway: N-Glycan biosynthesis - Homo sapiens (human);Mannose type O-glycan biosynthesis - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.139

Intolerance Scores

• loftool: 0.503
• rvis_EVS: -0.93
• rvis_percentile_EVS: 9.75

Haploinsufficiency Scores

• pHI: 0.257
• hipred: Y
• hipred_score: 0.685
• ghis: 0.647

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.538

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mgat5b
• Phenotype: reproductive system phenotype; hematopoietic system phenotype; skeleton phenotype; renal/urinary system phenotype; immune system 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); endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: protein N-linked glycosylation;protein O-linked glycosylation via serine
• Cellular component: Golgi membrane;Golgi apparatus;integral component of membrane
• Molecular function: protein binding;alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity;manganese ion binding