B4GALT7

beta-1,4-galactosyltransferase 7, the group of Beta 4-glycosyltransferases

Basic information

Region (hg38): 5:177600131-177610330

Links

ENSG00000027847 ∙ NCBI:11285 ∙ OMIM:604327 ∙ HGNC:930 ∙ Uniprot:Q9UBV7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Ehlers-Danlos syndrome, spondylodysplastic type, 1 (Definitive), mode of inheritance: AR
• Ehlers-Danlos syndrome, spondylodysplastic type, 1 (Strong), mode of inheritance: AR
• Ehlers-Danlos syndrome, spondylodysplastic type, 1 (Strong), mode of inheritance: AR
• Ehlers-Danlos syndrome, spondylodysplastic type, 1 (Moderate), mode of inheritance: AR
• Ehlers-Danlos syndrome, spondylodysplastic type, 1 (Strong), mode of inheritance: AR
• Ehlers-Danlos syndrome, spondylodysplastic type (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Ehlers-Danlos syndrome, spondylodysplastic type, 1	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; Dermatologic; Musculoskeletal; Neurologic	3631078; 10473568; 10506123; 15211654; 16583246; 20809901; 24755949

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the B4GALT7 gene.

• Ehlers-Danlos syndrome progeroid type (180 variants)
• not provided (92 variants)
• - (39 variants)
• Inborn genetic diseases (24 variants)
• not specified (19 variants)
• Ehlers-Danlos syndrome (14 variants)
• Ehlers-Danlos syndrome, spondylodysplastic type, 1 (14 variants)
• Lethal skeletal dysplasia (2 variants)
• (1 variants)
• Larsen-like syndrome, B3GAT3 type (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the B4GALT7 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			2	66	3	71
missense	1	1	126	1		129
nonsense			2			2
start loss						0
frameshift		1	5			6
inframe indel			1			1
splice donor/acceptor (+/-2bp)			3			3
splice region			6	7		13
non coding			1	41	19	61
Total	1	2	140	108	22

Highest pathogenic variant AF is 0.0000788

Variants in B4GALT7

This is a list of pathogenic ClinVar variants found in the B4GALT7 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-177600175-G-A		not specified	Likely benign (Aug 01, 2017)
5-177600180-C-T		not specified	Likely benign (Feb 23, 2017)
5-177600183-G-T		not specified	Likely benign (Nov 15, 2017)
5-177600185-C-T		not specified	Likely benign (Jan 30, 2018)
5-177600194-C-A		not specified	Likely benign (Sep 28, 2017)
5-177600217-C-T		Ehlers-Danlos syndrome progeroid type	Uncertain significance (Aug 09, 2022)
5-177600223-C-T		Ehlers-Danlos syndrome progeroid type	Uncertain significance (Nov 23, 2021)
5-177600225-G-A		Ehlers-Danlos syndrome progeroid type	Likely benign (Dec 22, 2023)
5-177600228-G-A		Ehlers-Danlos syndrome progeroid type	Likely benign (Jan 25, 2024)
5-177600230-A-G		Inborn genetic diseases • Ehlers-Danlos syndrome progeroid type	Uncertain significance (Nov 08, 2022)
5-177600237-G-A		Ehlers-Danlos syndrome progeroid type	Likely benign (Oct 21, 2022)
5-177600239-A-T		Ehlers-Danlos syndrome progeroid type	Uncertain significance (Dec 29, 2021)
5-177600243-G-A		Ehlers-Danlos syndrome progeroid type	Likely benign (Mar 23, 2022)
5-177600245-C-T			Uncertain significance (May 30, 2014)
5-177600248-G-A		Ehlers-Danlos syndrome progeroid type • Ehlers-Danlos syndrome • Ehlers-Danlos syndrome, spondylodysplastic type, 1	Conflicting classifications of pathogenicity (Nov 13, 2023)
5-177600256-G-C		Ehlers-Danlos syndrome progeroid type	Uncertain significance (Jan 19, 2024)
5-177600259-A-G		Inborn genetic diseases • Ehlers-Danlos syndrome progeroid type	Uncertain significance (Feb 15, 2023)
5-177600261-G-A		Ehlers-Danlos syndrome progeroid type	Uncertain significance (Aug 21, 2022)
5-177600264-A-AGCG		Ehlers-Danlos syndrome progeroid type	Likely benign (Apr 16, 2022)
5-177600269-C-T		Ehlers-Danlos syndrome progeroid type	Likely benign (Feb 22, 2023)
5-177600273-G-T		Ehlers-Danlos syndrome progeroid type	Likely benign (Jul 08, 2022)
5-177600274-G-A		Ehlers-Danlos syndrome progeroid type	Likely benign (Dec 15, 2023)
5-177600280-C-A		Ehlers-Danlos syndrome progeroid type	Likely benign (May 11, 2023)
5-177600404-T-C			Benign (Jun 26, 2018)
5-177604159-C-G		Ehlers-Danlos syndrome progeroid type	Likely benign (Mar 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
B4GALT7	protein_coding	protein_coding	ENST00000029410	6	10248

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000113	0.838	125665	0	83	125748	0.000330

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.311	227	214	1.06	0.0000142	2112
Missense in Polyphen		99	94.511	1.0475		912
Synonymous	-0.583	97	90.0	1.08	0.00000603	667
Loss of Function	1.28	8	13.0	0.615	5.60e-7	145

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000745	0.000731
Ashkenazi Jewish	0.00	0.00
East Asian	0.000983	0.000979
Finnish	0.000463	0.000462
European (Non-Finnish)	0.000236	0.000220
Middle Eastern	0.000983	0.000979
South Asian	0.000524	0.000523
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for the biosynthesis of the tetrasaccharide linkage region of proteoglycans, especially for small proteoglycans in skin fibroblasts. {ECO:0000269|PubMed:24052259}.
• 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)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.413
• rvis_EVS: -0.73
• rvis_percentile_EVS: 14.02

Haploinsufficiency Scores

• pHI: 0.279
• hipred: N
• hipred_score: 0.204
• ghis: 0.591

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.108

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: B4galt7

Zebrafish Information Network

• Gene name: b4galt7
• Affected structure: cranial cartilage
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: carbohydrate metabolic process;glycosaminoglycan biosynthetic process;proteoglycan metabolic process;cellular protein modification process;protein N-linked glycosylation;glycosaminoglycan metabolic process;negative regulation of fibroblast proliferation;supramolecular fiber organization
• Cellular component: Golgi membrane;Golgi apparatus;integral component of membrane;Golgi cisterna membrane
• Molecular function: beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity;protein binding;galactosyltransferase activity;manganese ion binding;xylosylprotein 4-beta-galactosyltransferase activity