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.

not_specified (109 variants)
not_provided (5 variants)

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. These statistics are base on transcript: NM_001199172.2. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				3 clinvar		3
missense			94 clinvar	4 clinvar		98
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	95	7	0

Loading clinvar variants...

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