Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	2583
Gene name	Beta-1,4-N-acetyl-galactosaminyltransferase 1
Gene symbol	B4GALNT1
Synonyms (NCBI Gene)	GALGTGALNACTGalNAc-TSPG26
Chromosome	12
Chromosome location	12q13.3
Summary	GM2 and GD2 gangliosides are sialic acid-containing glycosphingolipids. GalNAc-T is the enzyme involved in the biosynthesis of G(M2) and G(D2) glycosphingolipids. GalNAc-T catalyzes the transfer of GalNAc into G(M3) and G(D3) by a beta-1,4 linkage, result

Show/Hide all (8)

SNP ID	Visualize variation	Clinical significance	Consequence
rs377445018	C>T	Likely-pathogenic	Splice donor variant
rs398122382	G>A	Pathogenic	Stop gained, non coding transcript variant, coding sequence variant, 5 prime UTR variant
rs745744124	C>-,CC	Likely-pathogenic, pathogenic	Coding sequence variant, 5 prime UTR variant, intron variant, frameshift variant, non coding transcript variant
rs766591558	G>-	Pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant, 5 prime UTR variant
rs879255241	G>A	Pathogenic	5 prime UTR variant, stop gained, non coding transcript variant, coding sequence variant, intron variant
rs879255242	T>G	Pathogenic	Non coding transcript variant, coding sequence variant, genic downstream transcript variant, missense variant
rs1361370524	G>A,C,T	Pathogenic	5 prime UTR variant, synonymous variant, coding sequence variant, non coding transcript variant, stop gained, intron variant, missense variant
rs1555186937	G>-	Likely-pathogenic	Frameshift variant, non coding transcript variant, 5 prime UTR variant, coding sequence variant

Show/Hide all (59)

miRTarBase ID	miRNA	Experiments
MIRT813458	hsa-miR-2467-3p	CLIP-seq
MIRT813459	hsa-miR-3678-3p	CLIP-seq
MIRT813460	hsa-miR-4310	CLIP-seq
MIRT1940489	hsa-miR-1236	CLIP-seq
MIRT1940490	hsa-miR-2113	CLIP-seq
MIRT813458	hsa-miR-2467-3p	CLIP-seq
MIRT1940491	hsa-miR-28-5p	CLIP-seq
MIRT1940492	hsa-miR-3139	CLIP-seq
MIRT1940493	hsa-miR-3183	CLIP-seq
MIRT1940494	hsa-miR-3670	CLIP-seq
MIRT813459	hsa-miR-3678-3p	CLIP-seq
MIRT1940495	hsa-miR-3925-3p	CLIP-seq
MIRT1940496	hsa-miR-4279	CLIP-seq
MIRT813460	hsa-miR-4310	CLIP-seq
MIRT1940497	hsa-miR-4420	CLIP-seq
MIRT1940498	hsa-miR-4723-3p	CLIP-seq
MIRT1940499	hsa-miR-515-5p	CLIP-seq
MIRT1940500	hsa-miR-665	CLIP-seq
MIRT1940501	hsa-miR-708	CLIP-seq
MIRT1940502	hsa-miR-766	CLIP-seq
MIRT1940503	hsa-miR-942	CLIP-seq
MIRT2179477	hsa-miR-1207-5p	CLIP-seq
MIRT2179478	hsa-miR-1343	CLIP-seq
MIRT2179479	hsa-miR-1913	CLIP-seq
MIRT2179480	hsa-miR-3074-5p	CLIP-seq
MIRT2179481	hsa-miR-3173-3p	CLIP-seq
MIRT2179482	hsa-miR-3189-5p	CLIP-seq
MIRT2179483	hsa-miR-324-3p	CLIP-seq
MIRT2179484	hsa-miR-4695-5p	CLIP-seq
MIRT2179485	hsa-miR-4722-3p	CLIP-seq
MIRT2179486	hsa-miR-4736	CLIP-seq
MIRT2179487	hsa-miR-4758-3p	CLIP-seq
MIRT2179488	hsa-miR-4763-3p	CLIP-seq
MIRT1940503	hsa-miR-942	CLIP-seq
MIRT2179478	hsa-miR-1343	CLIP-seq
MIRT1940490	hsa-miR-2113	CLIP-seq
MIRT813458	hsa-miR-2467-3p	CLIP-seq
MIRT813459	hsa-miR-3678-3p	CLIP-seq
MIRT2384705	hsa-miR-3978	CLIP-seq
MIRT813460	hsa-miR-4310	CLIP-seq
MIRT1940490	hsa-miR-2113	CLIP-seq
MIRT813458	hsa-miR-2467-3p	CLIP-seq
MIRT813459	hsa-miR-3678-3p	CLIP-seq
MIRT813460	hsa-miR-4310	CLIP-seq
MIRT2179477	hsa-miR-1207-5p	CLIP-seq
MIRT2179478	hsa-miR-1343	CLIP-seq
MIRT1940490	hsa-miR-2113	CLIP-seq
MIRT813458	hsa-miR-2467-3p	CLIP-seq
MIRT813459	hsa-miR-3678-3p	CLIP-seq
MIRT2384705	hsa-miR-3978	CLIP-seq
MIRT813460	hsa-miR-4310	CLIP-seq
MIRT2482935	hsa-miR-4323	CLIP-seq
MIRT2179486	hsa-miR-4736	CLIP-seq
MIRT2179488	hsa-miR-4763-3p	CLIP-seq
MIRT1940490	hsa-miR-2113	CLIP-seq
MIRT813458	hsa-miR-2467-3p	CLIP-seq
MIRT813459	hsa-miR-3678-3p	CLIP-seq
MIRT813460	hsa-miR-4310	CLIP-seq
MIRT2482935	hsa-miR-4323	CLIP-seq

Show/Hide all (33)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000139	Component	Golgi membrane	IEA
GO:0000139	Component	Golgi membrane	ISS
GO:0000139	Component	Golgi membrane	TAS
GO:0001574	Process	Ganglioside biosynthetic process	IBA
GO:0001574	Process	Ganglioside biosynthetic process	IDA	7487055, 7890749
GO:0001574	Process	Ganglioside biosynthetic process	IEA
GO:0001574	Process	Ganglioside biosynthetic process	IMP	1601877
GO:0003947	Function	(N-acetylneuraminyl)-galactosylglucosylceramide N-acetylgalactosaminyltransferase activity	IDA	7487055, 7890749
GO:0003947	Function	(N-acetylneuraminyl)-galactosylglucosylceramide N-acetylgalactosaminyltransferase activity	IEA
GO:0003947	Function	(N-acetylneuraminyl)-galactosylglucosylceramide N-acetylgalactosaminyltransferase activity	IMP	1601877
GO:0003947	Function	(N-acetylneuraminyl)-galactosylglucosylceramide N-acetylgalactosaminyltransferase activity	TAS	8702839
GO:0005794	Component	Golgi apparatus	IEA
GO:0005794	Component	Golgi apparatus	ISS
GO:0005975	Process	Carbohydrate metabolic process	TAS	1601877
GO:0006629	Process	Lipid metabolic process	IEA
GO:0006665	Process	Sphingolipid metabolic process	IEA
GO:0006687	Process	Glycosphingolipid metabolic process	IEA
GO:0006687	Process	Glycosphingolipid metabolic process	TAS	1601877
GO:0007033	Process	Vacuole organization	IEA
GO:0007283	Process	Spermatogenesis	IEA
GO:0008340	Process	Determination of adult lifespan	IEA
GO:0008376	Function	Acetylgalactosaminyltransferase activity	IBA
GO:0008376	Function	Acetylgalactosaminyltransferase activity	IEA
GO:0016020	Component	Membrane	IEA
GO:0016020	Component	Membrane	TAS	1601877
GO:0016740	Function	Transferase activity	IEA
GO:0016757	Function	Glycosyltransferase activity	IEA
GO:0016758	Function	Hexosyltransferase activity	IEA
GO:0019915	Process	Lipid storage	IEA
GO:0021675	Process	Nerve development	IEA
GO:0060173	Process	Limb development	IEA
GO:0061744	Process	Motor behavior	IEA
GO:1901137	Process	Carbohydrate derivative biosynthetic process	IEA

MIM	HGNC	e!Ensembl
601873	4117	ENSG00000135454

Q00973

Protein name

Beta-1,4 N-acetylgalactosaminyltransferase 1 (EC 2.4.1.92) ((N-acetylneuraminyl)-galactosylglucosylceramide) (GM2/GD2 synthase) (GalNAc-T)

Protein function

Involved in the biosynthesis of gangliosides GM2, GD2, GT2 and GA2 from GM3, GD3, GT3 and GA3, respectively.

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00535	Glycos_transf_2	280 → 450	Glycosyl transferase family 2	Family

Sequence

MWLGRRALCALVLLLACASLGLLYASTRDAPGLRLPLAPWAPPQSPRRPELPDLAPEPRY
AHIPVRIKEQVVGLLAWNNCSCESSGGGLPLPFQKQVRAIDLTKAFDPAELRAASATREQ
EFQAFLSRSQSPADQLLIAPANSPLQYPLQGVEVQPLRSILVPGLSLQAASGQEVYQVNL
TASLGTWDVAGEVTGVTLTGEGQADLTLVSPGLDQLNRQLQLVTYSSRSYQTNTADTVRF
STEGHEAAFTIRIRHPPNPRLYPPGSLPQGAQYNISALVTIATKTFLRYDRLRALITSIR
RFYPTVTVVIADDSDKPERVSGPYVEHYLMPFGKGWFAGRNLAVSQVTTKYVLWVDDDFV
FTARTRLERLVDVLERTPLDLVGGAVREISGFATTYRQLLSVEPGAPGLGNCLRQRRGFH
HELVGFPGCVVTDGVVNFFLARTDKVREVGFDPRLSRVAHLEFFLDGLGSLRVGSCSDVV
VDHASKLKLPWTSRDAGAETYARYRYPGSLDESQMAKHRLLFFKHRLQCMTSQ

Sequence length

533

Interactions

View interactions

	KEGG		Reactome
	Sphingolipid metabolism Glycosphingolipid biosynthesis - ganglio series Metabolic pathways		Glycosphingolipid metabolism

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (3)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Hereditary spastic paraplegia 26	Pathogenic; Likely pathogenic	rs2540668608, rs2540668999, rs563575730, rs766591558, rs398122382, rs745744124, rs879255241, rs879255242, rs1885117995, rs1884842111, rs759528128	RCV003317810 RCV003333451 RCV003988715 RCV000054419 RCV000054420 View all (6 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Spastic paraparesis	Likely pathogenic; Pathogenic	rs1884842111	RCV005241247	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Spastic paraplegia	Pathogenic; Likely pathogenic	rs144887664, rs371013292, rs745744124, rs1410753769, rs1296877590, rs1269140893, rs2540667597, rs1423595663, rs2540658045, rs2540640409, rs774736480, rs377445018, rs1555186937, rs1361370524, rs398122382, rs1340636078, rs1885117995 View all (2 more)	RCV001387496 RCV002568203 RCV002035395 RCV002007570 RCV003067995 View all (13 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (13)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
AUTISTIC DISORDER	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTOSOMAL RECESSIVE SPASTIC PARAPLEGIA TYPE 26	—	Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
B4GALNT1-related disorder	Conflicting classifications of pathogenicity; Likely benign; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COMPLEX HEREDITARY SPASTIC PARAPLEGIA	—	ClinGen, Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COMPLICATED HEREDITARY SPASTIC PARAPLEGIA	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
IMMUNE SYSTEM DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MAJOR DEPRESSIVE DISORDER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPASTIC PARAPLEGIA 26, AUTOSOMAL RECESSIVE	—	CTD, Disgenet, HPO CTD, Disgenet, HPO CTD, Disgenet, HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPASTIC PARAPLEGIA, HEREDITARY	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (53)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Alzheimer Disease	Alzheimer disease	Pubtator	32310165	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Autosomal recessive spastic paraplegia type 26	Spastic Paraplegia	Orphanet			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Carcinogenesis	Carcinogenesis	Pubtator	35935585	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	15178323	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma, Ovarian Epithelial	Ovarian Epithelial carcinoma	BEFREE	27095597, 29039611		★★★★★ ★☆☆☆☆ Found in Text Mining only
Cataract	Cataract	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Cerebral cortical atrophy	Cerebral cortical atrophy	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Cerebral Palsy	Cerebral palsy	Pubtator	35775650	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Chronic Lymphocytic Leukemia	Lymphocytic Leukemia	BEFREE	24076351		★★★★★ ★☆☆☆☆ Found in Text Mining only
Complicated hereditary spastic paraplegia	Spastic paraplegia	BEFREE	29983310		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Conventional (Clear Cell) Renal Cell Carcinoma	Renal Carcinoma	BEFREE	31491435		★★★★★ ★☆☆☆☆ Found in Text Mining only
Coronary Artery Disease	Coronary artery disease	BEFREE	26714046		★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Insulin-Dependent	Diabetes Mellitus	BEFREE	19318031		★★★★★ ★☆☆☆☆ Found in Text Mining only
Distal amyotrophy	Distal amyotrophy	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Dysarthria	Dysarthria	Pubtator	35775650	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Dysarthria	Dysarthria	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Dyskinetic syndrome	Dyskinetic Syndrome	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Dysmorphic features	Dysmorphic Features	CLINVAR_DG	23746551, 24103911, 24283893		★★★★★ ★☆☆☆☆ Found in Text Mining only
Epithelial ovarian cancer	Ovarian cancer	BEFREE	27095597, 29039611		★★★★★ ★☆☆☆☆ Found in Text Mining only
Gastrointestinal Neoplasms	Gastrointestinal neoplasm	Pubtator	11856818	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioblastoma Multiforme	Glioblastoma	BEFREE	16866986		★★★★★ ★☆☆☆☆ Found in Text Mining only
Henoch-Schoenlein Purpura	Henoch-Schonlein Nephritis	BEFREE	29983310		★★★★★ ★☆☆☆☆ Found in Text Mining only
Hereditary Breast and Ovarian Cancer Syndrome	Hereditary breast and ovarian cancer syndrome	Pubtator	23479608	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	BEFREE	29747824		★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Intestinal Neoplasms	Intestinal Neoplasms	LHGDN	17119850		★★★★★ ★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	11914601		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant Childhood Neoplasm	Malignant Neoplasm	BEFREE	23136245		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of gastrointestinal tract	Malignant gastrointestinal tract tumors	BEFREE	7533654		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	11914601		★★★★★ ★☆☆☆☆ Found in Text Mining only
Mammary Neoplasms	Mammary Neoplasms	LHGDN	17119850		★★★★★ ★☆☆☆☆ Found in Text Mining only
Melanoma	Melanoma	Pubtator	15226334, 15817820, 16116595, 20371696, 8702839	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
melanoma	Melanoma	LHGDN	17119850		★★★★★ ★☆☆☆☆ Found in Text Mining only
melanoma	Melanoma	BEFREE	18982394, 24548412, 7487055		★★★★★ ★☆☆☆☆ Found in Text Mining only
Mild Mental Retardation	Mental retardation	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Mood swings	Mood swings	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	27095597, 29496042		★★★★★ ★☆☆☆☆ Found in Text Mining only
nervous system disorder	Nervous System Disorder	BEFREE	30521973		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neuroblastoma	Neuroblastoma	Pubtator	11485908, 8702839	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Neuroblastoma	Neuroblastoma	BEFREE	23136245, 30007008, 9930722		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neurodegenerative Diseases	Neurodegenerative disorder	Pubtator	24103911	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Osteosarcoma	Osteosarcoma	Pubtator	39311783	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Parkinson Disease	Parkinson disease	BEFREE	29747823		★★★★★ ★☆☆☆☆ Found in Text Mining only
Premature Menopause	Premature Menopause	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Pseudobulbar Palsy	Pseudobulbar Palsy	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Retinoblastoma	Retinoblastoma	Pubtator	36148636	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Scoliosis, unspecified	Scoliosis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Sensorimotor neuropathy	Sensorimotor neuropathy	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Spastic Paraplegia	Spastic Paraplegia	HPO_DG			★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Spastic Paraplegia Hereditary	Hereditary spastic paraplegia	Pubtator	23746551, 24103911, 33638609, 35775650	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Spastic Paraplegia, Hereditary	Spastic paraplegia	BEFREE	28536081, 29747824, 30521973		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Testicular hypogonadism	Testicular Hypogonadism	BEFREE	30521973		★★★★★ ★☆☆☆☆ Found in Text Mining only
Uterine Cervical Neoplasms	Uterine neoplasm	Pubtator	31847655	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only

B4GALNT1 (beta-1,4-N-acetyl-galactosaminyltransferase 1)