B4GALT6

protein-coding

beta-1,4-galactosyltransferase 6, the group of Beta 4-glycosyltransferases

Gene summary

This gene is one of seven beta-1,4-galactosyltransferase (beta4GalT) genes in human. They encode type II membrane-bound glycoproteins that appear to have exclusive specificity for the donor substrate UDP-galactose; all transfer galactose in a beta1,4 linkage to similar acceptor sugars: GlcNAc, Glc, and Xyl. Each beta4GalT has a distinct function in the biosynthesis of different glycoconjugates and saccharide structures. As type II membrane proteins, they have an N-terminal hydrophobic signal sequence that directs the protein to the Golgi apparatus and which then remains uncleaved to function as a transmembrane anchor. This gene produces multiple protein isoforms - some of which are predicted to lack the N-terminal hydrophobic signal sequence and transmembrane domain. By sequence similarity, the beta4GalTs form four groups: beta4GalT1 and beta4GalT2, beta4GalT3 and beta4GalT4, beta4GalT5 and beta4GalT6, and beta4GalT7. The canonical enzyme encoded by this gene is a lactosylceramide synthase important for glycolipid biosynthesis. [provided by RefSeq, Jan 2020]

MANE transcript

NM_004775.5

Inheritance

—

ClinVar variants

U:41B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.14

Max pathogenic AF

—

Genomic locus

chr18:31,622,246-31,685,836

External References & Databases

Ensembl (ENSG00000118276)

Transcript & Mutation Effects

hg38 • Region Span ~63.6 kb

Loading mutation effect viewer...

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 B4GALT6 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 37

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004775.5. 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						0
missense			37 clinvar		1 clinvar	38
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	41	0	1	42

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 24 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004775.5	RefSeq	NP_004766.2	9	MANE Select
ENST00000306851.10	Ensembl	ENSP00000306459.5	9	MANE Select
NM_001330570.3	RefSeq	NP_001317499.1	8	Standard
NM_001378109.1	RefSeq	NP_001365038.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Sphingolipid metabolism - Homo sapiens (human)
Sphingolipid Metabolism
Gaucher Disease
Globoid Cell Leukodystrophy
Metachromatic Leukodystrophy (MLD)

Biological Process

lactosylceramide biosynthetic process
carbohydrate metabolic process
protein glycosylation
keratan sulfate biosynthetic process

Molecular Function

beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity
galactosyltransferase activity
metal ion binding

Cellular Component

Golgi membrane
integral component of membrane
Golgi cisterna membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000306851
Coding exons: 9
Length: 63590
Individuals with no LoFs: 125735
Homozygous LoFs: 0
Heterozygous LoFs: 10
Defined: 125745
p: 0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.70	149	220	0.677	0.0000117	2530
Missense (PolyPhen)		37	73.576	0.50288		750
Synonymous	0.692	70	77.8	0.900	0.00000440	693
Loss of Function	3.63	3	20.9	0.144	0.00000113	248

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000053	0.000053	rare
South Asian	0.000066	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Required for the biosynthesis of glycosphingolipids. {ECO:0000269|PubMed:1551920, ECO:0000269|PubMed:3099851}.;

Recessive Scores

pRec: 0.267

Intolerance Scores

LoFtool: 0.424
RVIS EVS: 0.19
RVIS percentile EVS: 67.03

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.865

Gene Damage Prediction

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