GALNT17

gene
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Also known as GALNTL3GalNAc-T5LGalNAc-T19GalNAc-T17ppGalNAc-T17

Summary

GALNT17 (polypeptide N-acetylgalactosaminyltransferase 17, HGNC:16347) is a protein-coding gene on chromosome 7q11.22, encoding Polypeptide N-acetylgalactosaminyltransferase 17 (Q6IS24). May catalyze 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.

This gene encodes an N-acetylgalactosaminyltransferase. This gene is located centromeric to the common deleted region in Williams-Beuren syndrome (WBS), a multisystem developmental disorder caused by the deletion of contiguous genes at 7q11.23. This protein may play a role in membrane trafficking.

Source: NCBI Gene 64409 — RefSeq curated summary.

At a glance

  • GWAS associations: 15
  • Clinical variants (ClinVar): 89 total
  • MANE Select transcript: NM_022479

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:16347
Approved symbolGALNT17
Namepolypeptide N-acetylgalactosaminyltransferase 17
Location7q11.22
Locus typegene with protein product
StatusApproved
AliasesGALNTL3, GalNAc-T5L, GalNAc-T19, GalNAc-T17, ppGalNAc-T17
Ensembl geneENSG00000185274
Ensembl biotypeprotein_coding
OMIM615137
Entrez64409

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 2 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000333538, ENST00000447516, ENST00000467723, ENST00000498380

RefSeq mRNA: 1 — MANE Select: NM_022479 NM_022479

CCDS: CCDS5540

Canonical transcript exons

ENST00000333538 — 11 exons

ExonStartEnd
ENSE000013038007171201871713599
ENSE000017055397113214471133040
ENSE000034686027166541171665596
ENSE000034875207167721171677306
ENSE000035373177133555071335733
ENSE000035588057141588971416063
ENSE000035615717142090871421105
ENSE000035723297171076171710928
ENSE000035900007166997271670109
ENSE000036808887157128571571402
ENSE000036890837138823571388401

Expression profiles

Bgee: expression breadth ubiquitous, 199 present calls, max score 97.43.

FANTOM5 (CAGE): breadth broad, TPM avg 3.8350 / max 82.4151, expressed in 500 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
789862.0951457
789891.2055343
789880.2329175
789870.2294150
2044740.072135

Top tissues by expression

249 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
trigeminal ganglionUBERON:000167597.43gold quality
dorsal root ganglionUBERON:000004496.89gold quality
cerebellar vermisUBERON:000472096.02gold quality
prefrontal cortexUBERON:000045195.35gold quality
right hemisphere of cerebellumUBERON:001489094.94gold quality
cerebellar cortexUBERON:000212994.90gold quality
cerebellar hemisphereUBERON:000224594.87gold quality
right frontal lobeUBERON:000281094.80gold quality
cerebellumUBERON:000203794.68gold quality
frontal cortexUBERON:000187094.44gold quality
Brodmann (1909) area 9UBERON:001354093.85gold quality
neocortexUBERON:000195093.27gold quality
apex of heartUBERON:000209893.23gold quality
dorsolateral prefrontal cortexUBERON:000983493.18gold quality
anterior cingulate cortexUBERON:000983592.59gold quality
tibial nerveUBERON:000132392.47gold quality
superior frontal gyrusUBERON:000266192.27gold quality
cerebral cortexUBERON:000095692.09gold quality
lateral nuclear group of thalamusUBERON:000273691.39gold quality
sural nerveUBERON:001548891.38gold quality
parietal lobeUBERON:000187290.96gold quality
heart left ventricleUBERON:000208490.92gold quality
cardiac ventricleUBERON:000208290.41gold quality
middle temporal gyrusUBERON:000277190.27gold quality
Ammon’s hornUBERON:000195490.21gold quality
occipital lobeUBERON:000202190.20gold quality
postcentral gyrusUBERON:000258190.08gold quality
primary visual cortexUBERON:000243689.47gold quality
ponsUBERON:000098889.06gold quality
left ventricle myocardiumUBERON:000656689.06gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-HCAD-25yes75.40
E-CURD-119yes47.07
E-ANND-3yes4.70

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

62 targeting GALNT17, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-8485100.0077.574731
HSA-MIR-4747-5P100.0067.902681
HSA-MIR-5196-5P100.0067.982761
HSA-MIR-4692100.0067.322066
HSA-MIR-656-3P100.0072.152788
HSA-MIR-451499.9967.101870
HSA-MIR-3692-3P99.9870.272139
HSA-MIR-7152-3P99.9767.47849
HSA-MIR-6778-3P99.9667.292693
HSA-MIR-302E99.9670.742669
HSA-MIR-6721-5P99.9368.922981
HSA-MIR-22-3P99.9368.13917
HSA-MIR-6768-5P99.9267.361942
HSA-MIR-302A-3P99.8971.231777
HSA-MIR-302B-3P99.8971.231777
HSA-MIR-302C-3P99.8971.201778
HSA-MIR-302D-3P99.8971.251777
HSA-MIR-444799.8567.812900
HSA-MIR-76599.8468.242442
HSA-MIR-11181-3P99.7566.382205
HSA-MIR-430699.7270.503630
HSA-MIR-6752-3P99.7266.711587
HSA-MIR-7-5P99.6770.531809
HSA-MIR-5007-3P99.5168.141242
HSA-MIR-143-3P99.4969.051457
HSA-MIR-477099.4969.091451
HSA-MIR-6727-3P99.4965.921333
HSA-MIR-203A-3P99.4970.562806
HSA-MIR-766-5P99.4767.912225
HSA-MIR-4722-3P99.3565.221099

Literature-anchored findings (GeneRIF, showing 5)

  • a subset of O-glycosylation produced by WBSCR17 controls dynamic membrane trafficking, probably between the cell surface and the late endosomes through macropinocytosis (PMID:22787146)
  • GWA study identified maternal genetic effects not previously identified in ASD at a locus in WBSCR17. (PMID:27876814)
  • Identification of Risk Loci for Parkinson Disease in Asians and Comparison of Risk Between Asians and Europeans: A Genome-Wide Association Study. (PMID:32310270)
  • Circ_WBSCR17 aggravates inflammatory responses and fibrosis by targeting miR-185-5p/SOX6 regulatory axis in high glucose-induced human kidney tubular cells. (PMID:32798559)
  • Parkinson’s Disease Risk Variant rs9638616 is Non-Specifically Associated with Altered Brain Structure and Function. (PMID:38640170)

Cross-species orthologs

16 orthologs

OrganismSymbolGene ID
danio_reriogalnt17ENSDARG00000042418
mus_musculusGalnt17ENSMUSG00000034040
rattus_norvegicusGalnt17ENSRNOG00000024435
drosophila_melanogasterPgant7FBGN0030930
drosophila_melanogasterPgant5FBGN0031681
drosophila_melanogasterPgant6FBGN0035375
drosophila_melanogasterCG7304FBGN0036527
drosophila_melanogasterCG7579FBGN0036528
drosophila_melanogasterPgant8FBGN0036529
drosophila_melanogasterPgant9FBGN0050463
drosophila_melanogasterCG31776FBGN0051776
drosophila_melanogasterPgant4FBGN0051956
caenorhabditis_elegansWBGENE00001628
caenorhabditis_elegansWBGENE00001630
caenorhabditis_elegansWBGENE00001632
caenorhabditis_elegansWBGENE00001635

Paralogs (19): GALNT16 (ENSG00000100626), GALNTL5 (ENSG00000106648), GALNT7 (ENSG00000109586), GALNT18 (ENSG00000110328), GALNT3 (ENSG00000115339), GALNT12 (ENSG00000119514), GALNT8 (ENSG00000130035), GALNT15 (ENSG00000131386), GALNT5 (ENSG00000136542), GALNT6 (ENSG00000139629), GALNT1 (ENSG00000141429), GALNT2 (ENSG00000143641), GALNT13 (ENSG00000144278), GALNT14 (ENSG00000158089), GALNT10 (ENSG00000164574), GALNTL6 (ENSG00000174473), GALNT11 (ENSG00000178234), GALNT9 (ENSG00000182870), GALNT4 (ENSG00000257594)

Protein

Protein identifiers

Polypeptide N-acetylgalactosaminyltransferase 17Q6IS24 (reviewed: Q6IS24)

Alternative names: Polypeptide GalNAc transferase-like protein 3, Protein-UDP acetylgalactosaminyltransferase-like protein 3, UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase-like protein 3, Williams-Beuren syndrome chromosomal region 17 protein

All UniProt accessions (3): Q6IS24, H7BZX9, Q2L4S5

UniProt curated annotations — full annotation on UniProt →

Function. May catalyze 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.

Subcellular location. Golgi apparatus membrane.

Tissue specificity. Highly expressed in brain and heart. Weakly expressed in kidney, liver, lung and spleen.

Disease relevance. WBSCR17 is located in the Williams-Beuren syndrome (WBS) critical region. WBS results from a hemizygous deletion of several genes on chromosome 7q11.23, thought to arise as a consequence of unequal crossing over between highly homologous low-copy repeat sequences flanking the deleted region.

Domain organisation. There are two conserved domains in the glycosyltransferase region: the N-terminal domain (domain A, also called GT1 motif), which is probably involved in manganese coordination and substrate binding and the C-terminal domain (domain B, also called Gal/GalNAc-T motif), which is probably involved in catalytic reaction and UDP-Gal binding. The ricin B-type lectin domain binds to GalNAc and contributes to the glycopeptide specificity.

Pathway. Protein modification; protein glycosylation.

Similarity. Belongs to the glycosyltransferase 2 family. GalNAc-T subfamily.

RefSeq proteins (1): NP_071924* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000772Ricin_B_lectinDomain
IPR001173Glyco_trans_2-likeDomain
IPR029044Nucleotide-diphossugar_transHomologous_superfamily
IPR035992Ricin_B-like_lectinsHomologous_superfamily
IPR045885GalNAc-TDomain

Pfam: PF00535, PF00652

Catalyzed reactions (Rhea), 2 shown:

  • L-seryl-[protein] + UDP-N-acetyl-alpha-D-galactosamine = a 3-O-[N-acetyl-alpha-D-galactosaminyl]-L-seryl-[protein] + UDP + H(+) (RHEA:23956)
  • L-threonyl-[protein] + UDP-N-acetyl-alpha-D-galactosamine = a 3-O-[N-acetyl-alpha-D-galactosaminyl]-L-threonyl-[protein] + UDP + H(+) (RHEA:52424)

UniProt features (23 total): binding site 7, disulfide bond 5, glycosylation site 3, topological domain 2, region of interest 2, chain 1, transmembrane region 1, sequence conflict 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q6IS24-F190.680.80

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (7): 248; 378; 381; 386; 192; 223; 246

Disulfide bonds (5): 142–373, 364–443, 478–494, 526–541, 568–586

Glycosylation sites (3): 50, 461, 486

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-913709O-linked glycosylation of mucins

MSigDB gene sets: 44 (showing top): GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, CATTTCA_MIR203, MYOD_01, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS, chr7q11, DOUGLAS_BMI1_TARGETS_UP, GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS, GOBP_PROTEIN_O_LINKED_GLYCOSYLATION, GOBP_GLYCOPROTEIN_METABOLIC_PROCESS, GRYDER_PAX3FOXO1_TOP_ENHANCERS, YGCGYRCGC_UNKNOWN, GOMF_ACETYLGALACTOSAMINYLTRANSFERASE_ACTIVITY, GOMF_HEXOSYLTRANSFERASE_ACTIVITY, GOMF_GLYCOSYLTRANSFERASE_ACTIVITY, GOMF_POLYPEPTIDE_N_ACETYLGALACTOSAMINYLTRANSFERASE_ACTIVITY

GO Biological Process (2): protein O-linked glycosylation (GO:0006493), obsolete protein glycosylation (GO:0006486)

GO Molecular Function (5): polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653), carbohydrate binding (GO:0030246), metal ion binding (GO:0046872), transferase activity (GO:0016740), glycosyltransferase activity (GO:0016757)

GO Cellular Component (3): Golgi membrane (GO:0000139), Golgi apparatus (GO:0005794), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
O-linked glycosylation1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
glycoprotein biosynthetic process1
acetylgalactosaminyltransferase activity1
catalytic activity, acting on a protein1
binding1
cation binding1
catalytic activity1
transferase activity1
Golgi apparatus1
bounding membrane of organelle1
cytoplasm1
endomembrane system1
intracellular membrane-bounded organelle1
cellular anatomical structure1

Protein interactions and networks

STRING

848 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
GALNT17CALN1Q9BXU9516
GALNT17AUTS2Q8WXX7475
GALNT17DLGAP4Q9Y2H0471
GALNT17METTL27Q8N6F8419
GALNT17CLMPQ9H6B4408
GALNT17B3GALNT2Q8NCR0406
GALNT17KCNK12Q9HB15404
GALNT17EOGTQ5NDL2403
GALNT17GTF2IP78347388
GALNT17GABRQQ9UN88374
GALNT17ZNF608Q9ULD9370
GALNT17MAN2C1Q9NTJ4351
GALNT17ASXL2Q76L83348
GALNT17CCNB3Q8WWL7348
GALNT17ECSCRQ19T08347
GALNT17RILPL1Q5EBL4347

IntAct

3 interactions, top by confidence:

ABTypeScore
TRDNTMEM223psi-mi:“MI:0914”(association)0.640
SAAL1TMEM223psi-mi:“MI:0914”(association)0.350

BioGRID (1): WBSCR17 (Synthetic Lethality)

ESM2 similar proteins: A4IGL7, D3ZB51, E9PZ19, O75882, O94779, O95970, P00533, P02469, P07942, P13590, P15209, P24503, P24786, P33150, P39038, P55245, P55283, P68500, P97300, P97527, P97546, Q01279, Q01973, Q03351, Q16288, Q16620, Q1EGL2, Q3B7N0, Q3UQ28, Q5IFJ9, Q5IS37, Q5IS82, Q5R945, Q63604, Q6IS24, Q6VNS1, Q7TPD3, Q7TT15, Q8K4Y5, Q8N475

Diamond homologs: A8Y236, H0ZAB5, O08832, O08912, O45293, O45947, O61394, O61397, O88422, P34678, P70419, Q07537, Q10471, Q10472, Q10473, Q14435, Q29121, Q49A17, Q5EA41, Q5RFJ6, Q6DJR8, Q6IS24, Q6P6V1, Q6P9A2, Q6P9S7, Q6PB93, Q6UE39, Q6WV16, Q6WV17, Q6WV19, Q6WV20, Q7K755, Q7TT15, Q7Z4T8, Q7Z7M9, Q80VA0, Q86SF2, Q86SR1, Q8BGT9, Q8BVG5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

89 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance72
Likely benign1
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

4747 predictions. Top by Δscore:

VariantEffectΔscore
7:71133036:GAATG:Gdonor_gain1.0000
7:71133039:TGGT:Tdonor_loss1.0000
7:71133040:GGTAA:Gdonor_loss1.0000
7:71133041:G:Cdonor_loss1.0000
7:71133042:T:Adonor_loss1.0000
7:71151820:A:AGacceptor_gain1.0000
7:71151821:G:GAacceptor_gain1.0000
7:71335545:TCTA:Tacceptor_loss1.0000
7:71335546:CTAG:Cacceptor_loss1.0000
7:71335547:TA:Tacceptor_loss1.0000
7:71335548:A:AGacceptor_gain1.0000
7:71335549:G:Aacceptor_loss1.0000
7:71335549:G:GGacceptor_gain1.0000
7:71335549:GGC:Gacceptor_gain1.0000
7:71335549:GGCT:Gacceptor_gain1.0000
7:71335549:GGCTT:Gacceptor_gain1.0000
7:71335729:ACCAA:Adonor_gain1.0000
7:71335730:CCAA:Cdonor_gain1.0000
7:71335730:CCAAG:Cdonor_loss1.0000
7:71335731:CAA:Cdonor_gain1.0000
7:71335732:AA:Adonor_gain1.0000
7:71335734:G:Cdonor_loss1.0000
7:71335734:G:GGdonor_gain1.0000
7:71335735:T:Adonor_loss1.0000
7:71388232:CA:Cacceptor_loss1.0000
7:71388233:A:AGacceptor_gain1.0000
7:71388233:AGGT:Aacceptor_gain1.0000
7:71388234:G:GCacceptor_gain1.0000
7:71388234:GGT:Gacceptor_gain1.0000
7:71388234:GGTG:Gacceptor_gain1.0000

AlphaMissense

3912 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
7:71335705:C:AR132S1.000
7:71335706:G:CR132P1.000
7:71388236:T:AC142S1.000
7:71388237:G:CC142S1.000
7:71388300:A:TE163V1.000
7:71388324:C:TS171F1.000
7:71416036:A:TD246V1.000
7:71416062:T:AW255R1.000
7:71416062:T:CW255R1.000
7:71420908:G:CW255C1.000
7:71420908:G:TW255C1.000
7:71421032:T:AW297R1.000
7:71421032:T:CW297R1.000
7:71421034:G:CW297C1.000
7:71421034:G:TW297C1.000
7:71571384:T:AN354K1.000
7:71571384:T:GN354K1.000
7:71665454:G:CR375P1.000
7:71665462:C:GH378D1.000
7:71665464:C:AH378Q1.000
7:71665464:C:GH378Q1.000
7:71665521:T:AN397K1.000
7:71665521:T:GN397K1.000
7:71665543:T:AW405R1.000
7:71665543:T:CW405R1.000
7:71677238:T:AC478S1.000
7:71677238:T:CC478R1.000
7:71677239:G:CC478S1.000
7:71677240:C:GC478W1.000
7:71710836:T:AC526S1.000

dbSNP variants (sampled 300 via entrez): RS1000002244 (7:71343661 A>G), RS1000009427 (7:71344192 C>G,T), RS1000017317 (7:71319346 G>A), RS1000024033 (7:71496590 G>A), RS1000024693 (7:71553889 C>T), RS1000027768 (7:71378776 G>C,T), RS1000037545 (7:71452497 A>G), RS1000039017 (7:71564601 C>A), RS1000043968 (7:71612485 G>A), RS1000053696 (7:71261938 C>T), RS1000056500 (7:71514900 T>G), RS1000061698 (7:71176748 T>A), RS1000063391 (7:71149243 A>T), RS1000066667 (7:71267041 A>G), RS1000067084 (7:71476307 C>T)

Disease associations

OMIM: gene MIM:615137 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

15 associations (top):

StudyTraitp-value
GCST001520_18Response to angiotensin II receptor blocker therapy2.000000e-06
GCST001850_28Major depressive disorder2.000000e-06
GCST002491_4Age-related hearing impairment2.000000e-06
GCST002979_2Response to montelukast in asthma (change in FEV1)9.000000e-07
GCST003264_963Post bronchodilator FEV1/FVC ratio5.000000e-06
GCST003901_13Cognitive decline (age-related)3.000000e-06
GCST004749_19Lung cancer in ever smokers8.000000e-06
GCST007003_2Cerebrospinal fluid p-tau levels in normal cognition2.000000e-07
GCST007006_5Logical memory (delayed recall) in normal cognition6.000000e-07
GCST007324_154Adventurousness1.000000e-12
GCST007327_60Smoking status (ever vs never smokers)3.000000e-08
GCST008161_67Waist circumference adjusted for body mass index7.000000e-06
GCST008223_2Diabetic peripheral neuropathy in type 2 diabetes3.000000e-06
GCST009391_375Metabolite levels8.000000e-06
GCST011920_1Hearing loss in noise exposure1.000000e-06

EFO canonical traits (8, from GWAS)

EFO IDTrait name
EFO:0005921FEV change measurement
EFO:0004713FEV/FVC ratio
EFO:0004763p-tau measurement
EFO:0004874memory performance
EFO:0008579risk-taking behaviour
EFO:0004318smoking behavior
EFO:0007789BMI-adjusted waist circumference
EFO:0010436triacylglycerol 56:9 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

PharmGKB clinical annotations

1 annotations.

VariantTypeLevelDrugsPhenotypes
rs7794356Efficacy3montelukastAsthma

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs7794356GALNT1730.001montelukast

CTD chemical–gene interactions

17 total (human), top 17 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, decreases expression, increases methylation4
trichostatin Adecreases expression1
arseniteincreases methylation1
2-palmitoylglycerolincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
belinostatdecreases expression1
dorsomorphinaffects cotreatment, decreases expression1
Resveratrolaffects cotreatment, decreases expression1
Sunitinibincreases expression1
Amiodaroneincreases expression1
Arsenicaffects methylation1
Doxorubicindecreases expression1
Leadaffects expression1
Plant Extractsaffects cotreatment, decreases expression1
Triclosanincreases expression1
Cyclosporinedecreases methylation1
Antirheumatic Agentsincreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.