GALNT12 (polypeptide N-acetylgalactosaminyltransferase 12)

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

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)

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:

Mucin type O-glycan biosynthesis
Other types of O-glycan biosynthesis
Metabolic pathways

Reactome:

Defective GALNT12 causes colorectal cancer 1 (CRCS1)
O-linked glycosylation of mucins

Associated diseases

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Adenomatous polyposis coli, attenuated	Conflicting classifications of pathogenicity	rs145236923	RCV000656380
Breast neoplasm	Conflicting classifications of pathogenicity	rs59362219	RCV001265633
Colorectal cancer	Uncertain significance	rs1472145598	RCV000590910
Colorectal cancer, susceptibility to, 1	Uncertain significance; Conflicting classifications of pathogenicity; Benign; Likely benign	rs1835406598, rs1316883841, rs1454775771, rs1272530441, rs868573205, rs1836406676, rs1443842231, rs1835404781, rs1427277664, rs1835864602, rs775040546, rs1835414006, rs955510774, rs200303625, rs757485456, rs1416100156, rs1465375485, rs374578939, rs766728145, rs920049418, rs143652350, rs1164208180, rs756834523, rs777942439, rs777089837, rs185007553, rs376150380, rs267606839, rs267606840, rs1588453974, rs1588453921, rs1401451719, rs1421429267, rs2490492227, rs1175927536, rs372616005, rs780705882, rs746381338, rs780883563, rs2490492765, rs1237226126, rs758830613, rs1441365263, rs1297555373, rs568933955, rs2490541238, rs752104260, rs2490454965, rs954825101, rs748116010, rs778289504, rs1431572320, rs1836485574, rs2490455022, rs2490542067, rs979207164, rs1836359052, rs1376691635, rs137917376, rs777152516, rs770337578, rs773270880, rs1457926819, rs2118450495, rs1313526292, rs1380223372, rs947412769, rs1272025858, rs1331475779, rs980755584, rs374167975, rs1835406027, rs1364225305, rs775453262, rs183981750, rs147356342, rs35616709, rs35632007, rs145236923, rs878855093, rs202137559, rs114902755, rs146834885, rs767946700, rs146690078, rs41306504, rs149726976, rs751386354, rs112898261, rs2490454875, rs1445032491, rs376894835, rs2490456496, rs1835409244, rs2490455316, rs1219900667, rs750758049, rs2490455206, rs2490502728, rs2490533531, rs2490516749, rs2490501834, rs1186370119, rs755708201, rs2490557795, rs2118355333, rs1836010425, rs1470109085, rs775275455, rs1485624295, rs2490456511, rs2490492142, rs2118254771, rs2490552125, rs2490501881, rs2490517033, rs2490541141, rs1374853820, rs988592123, rs1836409007, rs2490454942, rs752549319, rs780798931, rs2490455813, rs1836175199, rs2490566143, rs2118504921, rs1836168508, rs1836172586, rs889395877, rs2295923, rs59362219, rs150946638, rs773891669, rs79574929, rs150417178, rs748104709, rs1060502970, rs759843363, rs199958039, rs370705797, rs375844934, rs191834824, rs140471094, rs756614355, rs753534837, rs34565987, rs557604978, rs763057175, rs751874783, rs1060504773, rs16917929, rs776700061, rs10987768, rs367645298, rs148125332, rs898798901, rs145133746, rs370060387, rs202039153, rs769837927, rs1137654, rs779959875, rs371949942, rs1554753747, rs868590153, rs781089454, rs374994372, rs1285871027, rs370024536, rs777144221, rs759750251, rs772466597, rs751274362, rs376441206, rs1472145598, rs1186134407, rs956810048, rs1379414621, rs1040733256, rs1315923578, rs374545406, rs1259048855, rs1419382391, rs1009053405, rs1588436185, rs1437425266, rs866699148, rs751656135, rs140383365, rs747224942, rs1247073303, rs776800914, rs377671466, rs760069331, rs758330743, rs373792075, rs540061502, rs768925908, rs200420144, rs772292450, rs548915885, rs1234947730, rs762729583, rs145557511, rs777263033, rs1447125430, rs191693197, rs912533623, rs755796376, rs1588455792, rs139208509, rs200788044, rs764920800, rs751724626, rs142096902, rs374166991, rs368008649, rs764337232, rs146530383, rs367620732, rs1588461456, rs778081163, rs1237409974, rs1036085286, rs1289967555, rs267602051, rs756936867, rs1420976719, rs973765987, rs1017576138, rs756339026, rs1304764723, rs1196473648	RCV003462897 RCV002493699 RCV004570795 RCV004570751 RCV004570859 RCV003469578 RCV004570827 RCV005394983 RCV004570873 RCV005042619 RCV003464240 RCV004571680 RCV003471055 RCV003471107 RCV004571875 RCV003464267 RCV005397127 RCV004571888 RCV003464160 RCV004571130 RCV003464176 RCV004571674 RCV004571507 RCV003471040 RCV005397278 RCV005361985 RCV005361955 RCV000001332 RCV000001333 RCV000001334 RCV004572237 RCV004572245 RCV004572249 RCV005042811 RCV004572282 RCV003471351 RCV003464473 RCV003471344 RCV004572292 RCV004572300 RCV004572331 RCV004572311 RCV003471343 RCV005397396 RCV003464476 RCV004572343 RCV004572363 RCV005397405 RCV003464501 RCV003464508 RCV003465722 RCV003464519 RCV004572430 RCV003464504 RCV003465715 RCV003464513 RCV003465719 RCV005050572 RCV004572416 RCV003464522 RCV004572423 RCV004572448 RCV004572425 RCV003464535 RCV003465756 RCV003464540 RCV004571149 RCV005045206 RCV005399236 RCV005044984 RCV005356224 RCV003464644 RCV005399058 RCV004572708 RCV005049484 RCV003462385 RCV005396651 RCV005396668 RCV005396681 RCV005396818 RCV005396820 RCV005396821 RCV004567758 RCV003463682 RCV005396822 RCV005396823 RCV003463683 RCV004567759 RCV005396819 RCV004572867 RCV005399277 RCV003459823 RCV005047517 RCV005399336 RCV005399337 RCV003466069 RCV005399357 RCV003461629 RCV003461630 RCV003468239 RCV003461631 RCV003461632 RCV003461633 RCV003461634 RCV003468240 RCV003461635 RCV003468241 RCV003468242 RCV003468243 RCV003461637 RCV003461638 RCV003468244 RCV003461639 RCV003468245 RCV003461640 RCV003461641 RCV003468246 RCV003461642 RCV003461643 RCV004573278 RCV005040688 RCV005051449 RCV005392818 RCV004576643 RCV004576644 RCV004576645 RCV004576646 RCV004576647 RCV004576649 RCV004576650 RCV004576652 RCV004576653 RCV003463949 RCV005355910 RCV005398633 RCV005398668 RCV003463946 RCV002489130 RCV005398662 RCV003470473 RCV005398669 RCV003463950 RCV000766033 RCV003463945 RCV003463948 RCV000764795 RCV005398670 RCV005398667 RCV003470474 RCV003470471 RCV005398666 RCV005398663 RCV003463947 RCV004568059 RCV005398665 RCV005398664 RCV003470472 RCV005398909 RCV005398914 RCV005398911 RCV004569270 RCV005398915 RCV004569269 RCV005398913 RCV003459382 RCV003465260 RCV005398910 RCV005044856 RCV005398912 RCV003459380 RCV005398916 RCV003459381 RCV003459383 RCV000764794 RCV003465259 RCV005044855 RCV000764796 RCV000764797 RCV004569273 RCV004569271 RCV004569272 RCV000766032 RCV004568309 RCV003461272 RCV004569513 RCV003461166 RCV005047092 RCV003467432 RCV005392479 RCV005367606 RCV005049729 RCV004570033 RCV003467622 RCV003467654 RCV003461324 RCV003467614 RCV005394631 RCV003461386 RCV003467665 RCV003461394 RCV003467675 RCV004570032 RCV003461400 RCV003461401 RCV003461404 RCV004570059 RCV005394648 RCV003461420 RCV003461423 RCV004570081 RCV005394652 RCV003461426 RCV003461366 RCV004569966 RCV003467647 RCV004569970 RCV003467649 RCV003461370 RCV003461356 RCV003467637 RCV003461360 RCV004569960 RCV003467591 RCV004569871 RCV004569872 RCV004569876 RCV003467594 RCV003467595 RCV003461320 RCV004569894 RCV003461326 RCV004569899 RCV004569901 RCV004569905 RCV004569910 RCV004569912 RCV003461330 RCV004569974 RCV004799252 RCV004570306 RCV003462578 RCV004572398 RCV003469367 RCV005394812 RCV003462689 RCV003462676 RCV003462790 RCV003469436 RCV005040137 RCV005394927
Familial colorectal cancer	Conflicting classifications of pathogenicity	rs183981750	RCV001824686
Familial pancreatic carcinoma	Benign; Likely benign	rs2295923	RCV005899579
GALNT12-related disorder	Uncertain significance; Conflicting classifications of pathogenicity; Benign; Likely benign	rs1163186722, rs760180024, rs985361459, rs1457926819, rs183981750, rs35616709, rs145236923, rs568625965, rs878855093, rs149726976, rs751386354, rs752385211, rs2490557840, rs2490454410, rs1835403190, rs1060504772, rs59362219, rs150946638, rs201926457, rs150417178, rs146370762, rs1060504771, rs531023279, rs751874783, rs16917929, rs10987768, rs777028537, rs898798901, rs202039153, rs1137654, rs202043243, rs756809019, rs748389861, rs143860974, rs1588436068, rs768905490	RCV004731131 RCV003418311 RCV003958466 RCV004753562 RCV004752796 RCV003917844 RCV003937792 RCV004752810 RCV003897564 RCV003907894 RCV004752811 RCV003966333 RCV003402359 RCV003896658 RCV003984680 RCV003902707 RCV003970287 RCV003942565 RCV003401483 RCV003915312 RCV003925373 RCV004752907 RCV003942564 RCV003970348 RCV003960036 RCV003915313 RCV003925748 RCV004752950 RCV004752951 RCV003962636 RCV003980058 RCV003900279 RCV003900280 RCV003975332 RCV003908265 RCV003928388 RCV003928666 RCV003963029
Gastric cancer	Benign; Likely benign; Conflicting classifications of pathogenicity; Uncertain significance	rs2295923, rs753534837, rs756339026	RCV005899581 RCV005899493 RCV005909098
Hepatocellular carcinoma	Benign; Likely benign	rs2295923, rs200145205	RCV005899577 RCV005910962
Hereditary cancer-predisposing syndrome	Benign; Likely benign; Conflicting classifications of pathogenicity; Uncertain significance	rs3216734, rs764577272, rs77308018, rs145236923, rs202137559, rs41306504, rs751386354, rs2295923, rs773891669, rs16917929, rs1137654, rs2273846, rs369793331, rs1588461400	RCV005629648 RCV000209769 RCV000209141 RCV000210098 RCV005055009 RCV005055010 RCV005895381 RCV005055016 RCV005055015 RCV005055017 RCV005055018 RCV005055019 RCV001017171 RCV001012748
Malignant lymphoma, large B-cell, diffuse	Benign; Likely benign	rs2295923	RCV005899580
Malignant tumor of esophagus	Benign; Likely benign	rs2295923	RCV005899578
Melanoma	Conflicting classifications of pathogenicity	rs753534837	RCV005899494

Associations from Text Mining
Disease Name	Relationship Type	References
Adenocarcinoma	Associate	35046897
Adenoma	Associate	29095867
Attenuated familial adenomatous polyposis	Associate	29095867
Carcinogenesis	Associate	29095867
Colonic Neoplasms	Associate	20551049
Colorectal Neoplasms	Associate	20551049, 29749045
Galactosemias	Associate	33593824
Glomerulonephritis IGA	Associate	33593824
Inflammation	Associate	26448050
Lymphoma B Cell	Associate	26448050
Lymphoma Follicular	Associate	22473939
Neoplasms	Associate	20551049
Neoplastic Syndromes Hereditary	Associate	29095867
Pancreatic Neoplasms	Associate	39256447