GALNT12 (polypeptide N-acetylgalactosaminyltransferase 12)

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Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases Related genes Diseases linked via similar genes

Gene

• Entrez ID: 79695
• Gene name: Polypeptide N-acetylgalactosaminyltransferase 12
• Gene symbol: GALNT12
• Synonyms (NCBI Gene): CRCS1, GalNAc-T12
• Chromosome: 9
• Chromosome location: 9q22.33
• Summary: This gene encodes a member of a family of UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferases, which catalyze the transfer of N-acetylgalactosamine (GalNAc) from UDP-GalNAc to a serine or threonine residue on a polypeptide acceptor in the initial st

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs267606839	G>A,T	Uncertain-significance, risk-factor	Initiator codon variant, missense variant, genic upstream transcript variant, upstream transcript variant
rs267606840	C>A,T	Risk-factor	Missense variant, coding sequence variant
rs1588453974	C>G	Risk-factor	Coding sequence variant, stop gained

miRNA Show/Hide all (77)

miRTarBase ID	miRNA	Experiments	Reference
MIRT016888	hsa-miR-335-5p	Microarray	18185580
MIRT024339	hsa-miR-215-5p	Microarray	19074876
MIRT026189	hsa-miR-192-5p	Microarray	19074876
MIRT1010808	hsa-let-7a	CLIP-seq
MIRT1010809	hsa-let-7b	CLIP-seq
MIRT1010810	hsa-let-7c	CLIP-seq
MIRT1010811	hsa-let-7d	CLIP-seq
MIRT1010812	hsa-let-7e	CLIP-seq
MIRT1010813	hsa-let-7f	CLIP-seq
MIRT1010814	hsa-let-7g	CLIP-seq
MIRT1010815	hsa-let-7i	CLIP-seq
MIRT1010816	hsa-miR-1256	CLIP-seq
MIRT1010817	hsa-miR-139-5p	CLIP-seq
MIRT1010818	hsa-miR-202	CLIP-seq
MIRT1010819	hsa-miR-21	CLIP-seq
MIRT1010820	hsa-miR-23a	CLIP-seq
MIRT1010821	hsa-miR-23b	CLIP-seq
MIRT1010822	hsa-miR-23c	CLIP-seq
MIRT1010823	hsa-miR-361-5p	CLIP-seq
MIRT1010824	hsa-miR-4458	CLIP-seq
MIRT1010825	hsa-miR-4500	CLIP-seq
MIRT1010826	hsa-miR-4678	CLIP-seq
MIRT1010827	hsa-miR-520d-5p	CLIP-seq
MIRT1010828	hsa-miR-524-5p	CLIP-seq
MIRT1010829	hsa-miR-590-5p	CLIP-seq
MIRT1010830	hsa-miR-98	CLIP-seq
MIRT1999364	hsa-miR-1264	CLIP-seq
MIRT1999365	hsa-miR-149	CLIP-seq
MIRT1010823	hsa-miR-361-5p	CLIP-seq
MIRT2233023	hsa-miR-103a	CLIP-seq
MIRT2233024	hsa-miR-107	CLIP-seq
MIRT2233025	hsa-miR-1301	CLIP-seq
MIRT2233026	hsa-miR-15a	CLIP-seq
MIRT2233027	hsa-miR-15b	CLIP-seq
MIRT2233028	hsa-miR-16	CLIP-seq
MIRT2233029	hsa-miR-195	CLIP-seq
MIRT2233030	hsa-miR-27a	CLIP-seq
MIRT2233031	hsa-miR-27b	CLIP-seq
MIRT2233032	hsa-miR-424	CLIP-seq
MIRT2233033	hsa-miR-4698	CLIP-seq
MIRT2233034	hsa-miR-497	CLIP-seq
MIRT2233035	hsa-miR-5047	CLIP-seq
MIRT2233036	hsa-miR-513a-5p	CLIP-seq
MIRT2536852	hsa-miR-1179	CLIP-seq
MIRT2536853	hsa-miR-122	CLIP-seq
MIRT1010816	hsa-miR-1256	CLIP-seq
MIRT1010817	hsa-miR-139-5p	CLIP-seq
MIRT2536854	hsa-miR-140-5p	CLIP-seq
MIRT2536855	hsa-miR-3117-5p	CLIP-seq
MIRT2536856	hsa-miR-3529	CLIP-seq
MIRT2536857	hsa-miR-3545-5p	CLIP-seq
MIRT2536858	hsa-miR-3659	CLIP-seq
MIRT2536859	hsa-miR-3662	CLIP-seq
MIRT2536860	hsa-miR-379	CLIP-seq
MIRT2536861	hsa-miR-4307	CLIP-seq
MIRT2536862	hsa-miR-4318	CLIP-seq
MIRT2536863	hsa-miR-4422	CLIP-seq
MIRT2536864	hsa-miR-4451	CLIP-seq
MIRT2536865	hsa-miR-4460	CLIP-seq
MIRT2536866	hsa-miR-4536	CLIP-seq
MIRT2536867	hsa-miR-4650-3p	CLIP-seq
MIRT2536868	hsa-miR-4691-3p	CLIP-seq
MIRT2536869	hsa-miR-4789-3p	CLIP-seq
MIRT2536870	hsa-miR-4802-5p	CLIP-seq
MIRT2536871	hsa-miR-487a	CLIP-seq
MIRT2536872	hsa-miR-548c-3p	CLIP-seq
MIRT2536852	hsa-miR-1179	CLIP-seq
MIRT2536853	hsa-miR-122	CLIP-seq
MIRT2536858	hsa-miR-3659	CLIP-seq
MIRT2536859	hsa-miR-3662	CLIP-seq
MIRT2536861	hsa-miR-4307	CLIP-seq
MIRT2536862	hsa-miR-4318	CLIP-seq
MIRT2536863	hsa-miR-4422	CLIP-seq
MIRT2536866	hsa-miR-4536	CLIP-seq
MIRT2536869	hsa-miR-4789-3p	CLIP-seq
MIRT2536870	hsa-miR-4802-5p	CLIP-seq
MIRT2536872	hsa-miR-548c-3p	CLIP-seq

Gene ontology (GO) Show/Hide all (17)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000139	Component	Golgi membrane	IEA
GO:0000139	Component	Golgi membrane	TAS
GO:0004653	Function	Polypeptide N-acetylgalactosaminyltransferase activity	IBA
GO:0004653	Function	Polypeptide N-acetylgalactosaminyltransferase activity	IEA
GO:0004653	Function	Polypeptide N-acetylgalactosaminyltransferase activity	TAS
GO:0005515	Function	Protein binding	IPI	28514442, 33961781
GO:0005794	Component	Golgi apparatus	IBA
GO:0005794	Component	Golgi apparatus	IEA
GO:0006486	Process	Protein glycosylation	IEA
GO:0006493	Process	Protein O-linked glycosylation	IBA
GO:0016020	Component	Membrane	IEA
GO:0016266	Process	Protein O-linked glycosylation via N-acetyl-galactosamine	IEA
GO:0016266	Process	Protein O-linked glycosylation via N-acetyl-galactosamine	TAS
GO:0016740	Function	Transferase activity	IEA
GO:0016757	Function	Glycosyltransferase activity	IEA
GO:0030246	Function	Carbohydrate binding	IEA
GO:0046872	Function	Metal ion binding	IEA

Other IDs

• MIM: 610290
• HGNC: 19877
• e!Ensembl: ENSG00000119514

Protein

• UniProt ID: Q8IXK2
• Protein name: Polypeptide N-acetylgalactosaminyltransferase 12 (EC 2.4.1.41) (Polypeptide GalNAc transferase 12) (GalNAc-T12) (pp-GaNTase 12) (Protein-UDP acetylgalactosaminyltransferase 12) (UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 12)
• Protein function: Catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. Has activity toward non-glycosylated peptides such as Muc5AC,
• PDB: 6PXU
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00535	Glycos_transf_2	139 → 322	Glycosyl transferase family 2	Family
  PF00652	Ricin_B_lectin	445 → 574	Ricin-type beta-trefoil lectin domain	Domain

• Tissue specificity: TISSUE SPECIFICITY: Widely expressed at different levels of expression. Highly expressed in digestive organs such as small intestine, stomach, pancreas and colon. Expressed at intermediate level in testis, thyroid gland and spleen. Weakly expressed in who
• Sequence:

  MWGRTARRRCPRELRRGREALLVLLALLALAGLGSVLRAQRGAGAGAAEPGPPRTPRPGR
  REPVMPRPPVPANALGARGEAVRLQLQGEELRLQEESVRLHQINIYLSDRISLHRRLPER
  WNPLCKEKKYDYDNLPRTSVIIAFYNEAWSTLLRTVYSVLETSPDILLEEVILVDDYSDR
  EHLKERLANELSGLPKVRLIRANKREGLVRARLLGASAARGDVLTFLDCHCECHEGWLEP
  LLQRIHEEESAVVCPVIDVIDWNTFEYLGNSGEPQIGGFDWRLVFTWHTVPERERIRMQS
  PVDVIRSPTMAGGLFAVSKKYFEYLGSYDTGMEVWGGENLEFSFRIWQCGGVLETHPCSH
  VGHVFPKQAPYSRNKALANSVRAAEVWMDEFKELYYHRNPRARLEPFGDVTERKQLRDKL
  QCKDFKWFLETVYPELHVPEDRPGFFGMLQNKGLTDYCFDYNPPDENQIVGHQVILYLCH
  GMGQNQFFEYTSQKEIRYNTHQPEGCIAVEAGMDTLIMHLCEETAPENQKFILQEDGSLF
  HEQSKKCVQAARKESSDSFVPLLRDCTNSDHQKWFFKERML

• Sequence length: 581

Pathways

KEGG Pathway	Reactome Pathway
Mucin type O-glycan biosynthesis	Defective GALNT12 causes colorectal cancer 1 (CRCS1)
Other types of O-glycan biosynthesis	O-linked glycosylation of mucins
Metabolic pathways

Associated diseases

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)

Unknown / Other Associations Show/Hide Unknown Diseases (18)
Phenotype Name	Clinical Significance	Source	Reference	Evidence Score
Adenomatous polyposis coli, attenuated	Conflicting classifications of pathogenicity	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ASTHMA	—	GWAS catalog	35104449	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATRIAL FIBRILLATION	—	GWAS catalog	40050429, 40645996	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTISM SPECTRUM DISORDER	—	GWAS catalog	34069769	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Breast neoplasm	Conflicting classifications of pathogenicity	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHRONIC OBSTRUCTIVE PULMONARY DISEASE	—	GWAS catalog	33106845, 35104449, 37069358	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colorectal cancer	Uncertain significance	ClinVar GWAS catalog	25866641	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Colorectal cancer, susceptibility to, 1	Uncertain significance; Conflicting classifications of pathogenicity; Benign; Likely benign	ClinVar ClinGen	ClinGen report	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
COLORECTAL NEOPLASMS	—	CTD	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial colorectal cancer	Conflicting classifications of pathogenicity	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial pancreatic carcinoma	Benign; Likely benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GALNT12-related disorder	Uncertain significance; Conflicting classifications of pathogenicity; Benign; Likely benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign; Likely benign; Conflicting classifications of pathogenicity; Uncertain significance	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Benign; Likely benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hereditary cancer-predisposing syndrome	Benign; Likely benign; Conflicting classifications of pathogenicity; Uncertain significance	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign; Likely benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign; Likely benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Melanoma	Conflicting classifications of pathogenicity	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining Show/Hide Text Mining Associations (21)
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Adenoma	Adenoma	BEFREE	29095867		★☆☆☆☆ Found in Text Mining only
Adenomatous Polyposis Coli	Multiple polyposis syndrome	BEFREE	29095867		★☆☆☆☆ Found in Text Mining only
Attenuated familial adenomatous polyposis	Adenomatous polyposis	Pubtator	29095867	Associate	★☆☆☆☆ Found in Text Mining only
bilateral breast cancer	Breast Cancer	BEFREE	24038392		★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Carcinogenesis	Pubtator	29095867	Associate	★☆☆☆☆ Found in Text Mining only
Colonic Neoplasms	Colonic neoplasm	Pubtator	20551049	Associate	★☆☆☆☆ Found in Text Mining only
Colonic Neoplasms	Colonic Neoplasms	BEFREE	20551049		★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	BEFREE	22461326, 24038392, 24115450, 29749045, 31548401		★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal Neoplasms	LHGDN	15557789		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	20551049, 29749045	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colorectal Neoplasms	Colorectal Neoplasms	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial Colorectal Cancer Type X	Colorectal Cancer	BEFREE	24115450		★☆☆☆☆ Found in Text Mining only
Galactosemias	Galactosemia	Pubtator	33593824	Associate	★☆☆☆☆ Found in Text Mining only
Glomerulonephritis IGA	Iga nephropathy	Pubtator	33593824	Associate	★☆☆☆☆ Found in Text Mining only
Lymphoma Follicular	Lymphoma	Pubtator	22473939	Associate	★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	22461326		★☆☆☆☆ Found in Text Mining only
Malignant tumor of colon	Colonic Neoplasms	BEFREE	19617566		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	24115450		★☆☆☆☆ Found in Text Mining only
Non-obstructive azoospermia	Non-obstructive azoospermia	GWASDB_DG	22197933		★☆☆☆☆ Found in Text Mining only
Pancreatic Neoplasms	Pancreatic neoplasm	Pubtator	39256447	Associate	★☆☆☆☆ Found in Text Mining only

Related Genes

Sort by: Blended Diseases Pathways Evidence source

POLE 2 shared diseasesColorectal cancer susceptibility, Colorectal neoplasms 3 shared evidence sourcesClinVar (Colorectal cancer susceptibility), GenCC (Colorectal cancer susceptibility), CTD (Colorectal neoplasms) Related via 2 shared diseases including Colorectal cancer susceptibility, Colorectal neoplasms — evidence mostly ClinVar. POC1B-GALNT4 3 shared pathwaysMucin type O-glycan biosynthesis, Other types of O-glycan biosynthesis, O-linked glycosylation of mucins Related via 3 shared pathways including Mucin type O-glycan biosynthesis, Other types of O-glycan biosynthesis. GALNT6 3 shared pathwaysMucin type O-glycan biosynthesis, Other types of O-glycan biosynthesis, O-linked glycosylation of mucins Related via 3 shared pathways including Mucin type O-glycan biosynthesis, Other types of O-glycan biosynthesis. GALNT5 3 shared pathwaysMucin type O-glycan biosynthesis, Other types of O-glycan biosynthesis, O-linked glycosylation of mucins Related via 3 shared pathways including Mucin type O-glycan biosynthesis, Other types of O-glycan biosynthesis. GALNT13 3 shared pathwaysMucin type O-glycan biosynthesis, Other types of O-glycan biosynthesis, O-linked glycosylation of mucins Related via 3 shared pathways including Mucin type O-glycan biosynthesis, Other types of O-glycan biosynthesis.

Related Gene	Shared Diseases	Shared Disease Names	Shared Pathways	Shared Pathway Names	Shared Evidence Sources	Shared Evidence Names
POLE	2	["Colorectal cancer susceptibility","Colorectal neoplasms"]	0	[]	3	["ClinVar (Colorectal cancer susceptibility)","GenCC (Colorectal cancer susceptibility)","CTD (Colorectal neoplasms)"]
POC1B-GALNT4	0	[]	3	["Mucin type O-glycan biosynthesis","Other types of O-glycan biosynthesis","O-linked glycosylation of mucins"]	0	[]
GALNT6	0	[]	3	["Mucin type O-glycan biosynthesis","Other types of O-glycan biosynthesis","O-linked glycosylation of mucins"]	0	[]
GALNT5	0	[]	3	["Mucin type O-glycan biosynthesis","Other types of O-glycan biosynthesis","O-linked glycosylation of mucins"]	0	[]
GALNT13	0	[]	3	["Mucin type O-glycan biosynthesis","Other types of O-glycan biosynthesis","O-linked glycosylation of mucins"]	0	[]

Diseases Linked via Similar Genes

Schizophrenia Linked via 3 of 5 related genesPOC1B-GALNT4, GALNT5, GALNT13 Metabolic syndrome Linked via 2 of 5 related genesPOC1B-GALNT4, GALNT13 Diabetes mellitus type 2 Linked via 2 of 5 related genesPOC1B-GALNT4, GALNT13 Constitutional mismatch repair deficiency Linked via 1 of 5 related genesPOLE Cystic fibrosis Linked via 1 of 5 related genesPOLE

Disease	Linked Via (Gene Count)	Linked Via (Gene Names)
Schizophrenia	3	["POC1B-GALNT4","GALNT5","GALNT13"]
Metabolic syndrome	2	["POC1B-GALNT4","GALNT13"]
Diabetes mellitus type 2	2	["POC1B-GALNT4","GALNT13"]
Constitutional mismatch repair deficiency	1	["POLE"]
Cystic fibrosis	1	["POLE"]