MGAT5B

protein-coding

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

Gene summary

Enables alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity and manganese ion binding activity. Involved in protein O-linked glycosylation. Predicted to be located in Golgi membrane. Predicted to be active in Golgi apparatus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001199172.2

Inheritance

—

ClinVar variants

U:115B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.28

Max pathogenic AF

—

Genomic locus

chr17:76,868,404-76,950,393

External References & Databases

Ensembl (ENSG00000167889)

Transcript & Mutation Effects

hg38 • Region Span ~82.0 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 MGAT5B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 125

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001199172.2. 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				3 clinvar		3
missense			111 clinvar	4 clinvar		115
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	115	7	0	122

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 22 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001199172.2	RefSeq	NP_001186101.1	18	MANE Select
ENST00000569840.7	Ensembl	ENSP00000456037.2	18	MANE Select
NM_144677.3	RefSeq	NP_653278.2	17	Standard
NM_198955.1	RefSeq	NP_945193.1	16	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

N-Glycan biosynthesis - Homo sapiens (human)
Mannose type O-glycan biosynthesis - Homo sapiens (human)

Biological Process

protein N-linked glycosylation
protein O-linked glycosylation via serine

Molecular Function

protein binding
alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity
manganese ion binding

Cellular Component

Golgi membrane
Golgi apparatus
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000428789
Coding exons: 16
Length: 81938
Individuals with no LoFs: 125726
Homozygous LoFs: 0
Heterozygous LoFs: 21
Defined: 125747
p: 0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.78	410	525	0.781	0.0000353	5196
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000064	0.000062	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0	0.0	absent
Finnish	0.000097	0.000092	rare
European (Non-Finnish)	0.000081	0.000079	rare
South Asian	0.00013	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.139

Intolerance Scores

LoFtool: 0.503
RVIS EVS: -0.93
RVIS percentile EVS: 9.75

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.538

Gene Damage Prediction

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