B3GALT6

beta-1,3-galactosyltransferase 6, the group of Beta 3-glycosyltransferases

Basic information

Region (hg38): 1:1232237-1235041

Links

ENSG00000176022 ∙ NCBI:126792 ∙ OMIM:615291 ∙ HGNC:17978 ∙ Uniprot:Q96L58 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spondyloepimetaphyseal dysplasia with joint laxity, type 1, with or without fractures (Definitive), mode of inheritance: AR
• Ehlers-Danlos syndrome, spondylodysplastic type, 2 (Strong), mode of inheritance: AR
• Ehlers-Danlos syndrome, spondylodysplastic type, 2 (Strong), mode of inheritance: AR
• spondyloepimetaphyseal dysplasia with joint laxity, type 1, with or without fractures (Strong), mode of inheritance: AR
• Ehlers-Danlos syndrome, spondylodysplastic type, 2 (Strong), mode of inheritance: AR
• spondyloepimetaphyseal dysplasia with joint laxity (Supportive), mode of inheritance: AR
• Ehlers-Danlos syndrome, spondylodysplastic type, 2 (Strong), mode of inheritance: AR
• spondyloepimetaphyseal dysplasia with joint laxity, type 1, with or without fractures (Strong), mode of inheritance: AR
• Ehlers-Danlos syndrome, spondylodysplastic type, 2 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Ehlers-Danlos syndrome, spondylodysplastic type, 2; Spondyloepimetaphyseal dysplasia with joint laxity, type 1, with or without fractures; Al-Gazali syndrome	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic	23664117; 23664118; 25149931; 29443383

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the B3GALT6 gene.

• Ehlers-Danlos_syndrome,_spondylodysplastic_type,_2 (275 variants)
• Spondyloepimetaphyseal_dysplasia_with_joint_laxity (264 variants)
• not_provided (110 variants)
• Inborn_genetic_diseases (71 variants)
• Spondyloepimetaphyseal_dysplasia_with_joint_laxity,_type_1,_with_or_without_fractures (24 variants)
• not_specified (22 variants)
• B3GALT6-related_disorder (17 variants)
• Al-Gazali_syndrome (10 variants)
• Spondyloepimetaphyseal_dysplasia_with_joint_laxity,_type_1,_with_fractures (4 variants)
• Spondyloepiphyseal_dysplasia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the B3GALT6 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000080605.4. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			6	108		114
missense	10	8	173	9	1	201
nonsense	2	5	2			9
start loss	3	3				6
frameshift	4	6	11			21
splice donor/acceptor (+/-2bp)						0
Total	19	22	192	117	1

Highest pathogenic variant AF is 0.000144797

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
B3GALT6	protein_coding	protein_coding	ENST00000379198	1	2793

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0227	0.779	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.26	93	134	0.694	0.0000112	1992
Missense in Polyphen		26	48.604	0.53493		698
Synonymous	0.413	61	65.2	0.935	0.00000586	751
Loss of Function	0.932	3	5.32	0.564	2.32e-7	77

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Beta-1,3-galactosyltransferase that transfers galactose from UDP-galactose to substrates with a terminal beta-linked galactose residue. Has a preference for galactose-beta-1,4-xylose that is found in the linker region of glycosaminoglycans, such as heparan sulfate and chondroitin sulfate. Has no activity towards substrates with terminal glucosamine or galactosamine residues. {ECO:0000269|PubMed:11551958}.
• Disease: DISEASE: Spondyloepimetaphyseal dysplasia with joint laxity, 1, with or without fractures (SEMDJL1) [MIM:271640]: A bone disease characterized by vertebral abnormalities and ligamentous laxity that result in spinal misalignment and progressive severe kyphoscoliosis, thoracic asymmetry, and respiratory compromise resulting in early death. Additional skeletal features include elbow deformities with radial head dislocation, dislocated hips, clubfeet, and tapered fingers with spatulate distal phalanges. Many affected children have an oval face, flat midface, prominent eyes with blue sclerae, and a long philtrum. Palatal abnormalities and congenital heart disease are also observed. {ECO:0000269|PubMed:23664117, ECO:0000269|PubMed:23664118}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate - Homo sapiens (human);Glycosaminoglycan biosynthesis - heparan sulfate / heparin - Homo sapiens (human);Metabolism of carbohydrates;A tetrasaccharide linker sequence is required for GAG synthesis;Heparan sulfate/heparin (HS-GAG) metabolism;Chondroitin sulfate/dermatan sulfate metabolism;Glycosaminoglycan metabolism;Proteoglycan biosynthesis;glycoaminoglycan-protein linkage region biosynthesis;chondroitin sulfate biosynthesis;heparan sulfate biosynthesis;dermatan sulfate biosynthesis;Metabolism (Consensus)

Haploinsufficiency Scores

• pHI: 0.153
• hipred: N
• hipred_score: 0.429
• ghis: 0.526

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.736

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: B3galt6

Gene ontology

• Biological process: glycosaminoglycan biosynthetic process;protein glycosylation;heparan sulfate proteoglycan biosynthetic process;glycosaminoglycan metabolic process;chondroitin sulfate biosynthetic process
• Cellular component: Golgi membrane;endoplasmic reticulum;Golgi apparatus;Golgi medial cisterna;membrane;integral component of membrane;Golgi cisterna membrane
• Molecular function: galactosyltransferase activity;UDP-galactosyltransferase activity;galactosylxylosylprotein 3-beta-galactosyltransferase activity