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WSCD2

gene
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Also known as KIAA0789

Summary

WSCD2 (WSC domain sialate O sulfotransferase 2, HGNC:29117) is a protein-coding gene on chromosome 12q23.3, encoding Sialate:O-sulfotransferase 2 (Q2TBF2). Sialate:O-sulfotransferase which catalyzes 8-O-sulfation at the Sia-glycan level using 3’-phosphoadenosine 5’-phosphosulfate (PAPS) as a donor, forming 8-O-sulfated Sia (Sia8S)-glycans.

Predicted to enable sulfotransferase activity. Predicted to be located in Golgi membrane.

Source: NCBI Gene 9671 — RefSeq curated summary.

At a glance

  • GWAS associations: 28
  • Clinical variants (ClinVar): 98 total
  • MANE Select transcript: NM_014653

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:29117
Approved symbolWSCD2
NameWSC domain sialate O sulfotransferase 2
Location12q23.3
Locus typegene with protein product
StatusApproved
AliasesKIAA0789
Ensembl geneENSG00000075035
Ensembl biotypeprotein_coding
OMIM619253
Entrez9671

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 8 protein_coding_CDS_not_defined, 7 protein_coding, 1 retained_intron

ENST00000332082, ENST00000546401, ENST00000546629, ENST00000546811, ENST00000547185, ENST00000547525, ENST00000549903, ENST00000550529, ENST00000551057, ENST00000551106, ENST00000551638, ENST00000551734, ENST00000552195, ENST00000854237, ENST00000854238, ENST00000854239

RefSeq mRNA: 2 — MANE Select: NM_014653 NM_001304447, NM_014653

CCDS: CCDS41828

Canonical transcript exons

ENST00000547525 — 9 exons

ExonStartEnd
ENSE00000938221108240344108240544
ENSE00001669802108224739108224860
ENSE00001722460108210121108210305
ENSE00001766844108232731108232895
ENSE00001774185108195282108196214
ENSE00002341368108247991108250537
ENSE00002343185108129288108129926
ENSE00003541687108226990108227164
ENSE00003584280108206289108206403

Expression profiles

Bgee: expression breadth ubiquitous, 177 present calls, max score 97.41.

FANTOM5 (CAGE): breadth broad, TPM avg 1.9190 / max 217.5672, expressed in 372 samples.

FANTOM5 promoters (11 alternative TSS)

Promoter IDTPM avgSamples expressed
1278670.6157162
1278700.2908108
1278710.194376
1278730.176786
1278750.146564
1278680.139864
1278690.124343
1278650.118554
1278740.044532
1278660.044022

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
cerebellar cortexUBERON:000212997.41gold quality
cerebellar hemisphereUBERON:000224597.38gold quality
cerebellumUBERON:000203797.28gold quality
right hemisphere of cerebellumUBERON:001489097.20gold quality
cerebellar vermisUBERON:000472096.60gold quality
middle temporal gyrusUBERON:000277193.17gold quality
tibiaUBERON:000097991.08gold quality
islet of LangerhansUBERON:000000689.21gold quality
Brodmann (1909) area 23UBERON:001355488.89gold quality
primary visual cortexUBERON:000243687.90gold quality
right lobe of thyroid glandUBERON:000111987.25gold quality
calcaneal tendonUBERON:000370187.06gold quality
thyroid glandUBERON:000204686.96gold quality
left lobe of thyroid glandUBERON:000112086.76gold quality
lower esophagus muscularis layerUBERON:003583385.94gold quality
lower esophagusUBERON:001347385.82gold quality
mucosa of stomachUBERON:000119985.26gold quality
prefrontal cortexUBERON:000045185.03gold quality
right frontal lobeUBERON:000281085.02gold quality
cartilage tissueUBERON:000241884.56gold quality
frontal cortexUBERON:000187084.34gold quality
nucleus accumbensUBERON:000188284.06gold quality
entorhinal cortexUBERON:000272884.06gold quality
occipital lobeUBERON:000202183.80gold quality
superior frontal gyrusUBERON:000266183.42gold quality
dorsolateral prefrontal cortexUBERON:000983483.04gold quality
Brodmann (1909) area 9UBERON:001354082.98gold quality
Brodmann (1909) area 46UBERON:000648382.95gold quality
neocortexUBERON:000195082.77gold quality
postcentral gyrusUBERON:000258182.59gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-MTAB-5061yes18.48
E-GEOD-83139yes10.02
E-ANND-3no4.86

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): NR1I2

miRNA regulators (miRDB)

92 targeting WSCD2, 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-7110-3P100.0073.182486
HSA-MIR-8485100.0077.574731
HSA-MIR-6873-3P100.0071.422626
HSA-MIR-6758-5P100.0066.211470
HSA-MIR-6856-5P100.0065.471298
HSA-MIR-4481100.0066.421669
HSA-MIR-5193100.0067.261744
HSA-MIR-4262100.0073.263931
HSA-MIR-4745-5P99.9865.951028
HSA-MIR-548AN99.9770.912817
HSA-MIR-6888-3P99.9765.951170
HSA-MIR-4725-3P99.9669.532520
HSA-MIR-6780B-5P99.9669.602562
HSA-MIR-211099.9666.681930
HSA-MIR-311999.9271.342390
HSA-MIR-6499-3P99.9066.381212
HSA-MIR-449399.9066.48977
HSA-MIR-605-3P99.8869.221833
HSA-MIR-427199.8868.322244
HSA-MIR-394199.8670.542735
HSA-MIR-444799.8567.812900
HSA-MIR-6817-3P99.7968.352126
HSA-MIR-4713-5P99.7867.801794
HSA-MIR-674599.7465.331321
HSA-MIR-4524A-3P99.7266.852406
HSA-MIR-1296-3P99.7264.04636
HSA-MIR-430699.7270.503630
HSA-MIR-3059-5P99.7069.932491
HSA-MIR-7154-5P99.6970.521900
HSA-MIR-1251-3P99.6467.211408

Literature-anchored findings (GeneRIF, showing 1)

  • WSCD2 polymorphism is associated with extraversion. (PMID:27918536)

Cross-species orthologs

22 orthologs

OrganismSymbolGene ID
danio_reriowscd2ENSDARG00000061819
mus_musculusWscd2ENSMUSG00000063430
rattus_norvegicusWscd2ENSRNOG00000053045
drosophila_melanogasteroxtFBGN0015360
drosophila_melanogasterCG9164FBGN0030634
caenorhabditis_elegansgly-15WBGENE00001640
caenorhabditis_elegansgly-16WBGENE00001641
caenorhabditis_elegansgly-17WBGENE00001642
caenorhabditis_elegansgly-18WBGENE00001643
caenorhabditis_elegansgly-19WBGENE00001644
caenorhabditis_elegansWBGENE00005024
caenorhabditis_elegansWBGENE00009148
caenorhabditis_elegansF30A10.4WBGENE00009263
caenorhabditis_elegansWBGENE00011090
caenorhabditis_elegansT09E11.6WBGENE00011655
caenorhabditis_elegansT09E11.9WBGENE00011658
caenorhabditis_elegansT27F6.1WBGENE00012102
caenorhabditis_elegansWBGENE00012135
caenorhabditis_elegansWBGENE00013119
caenorhabditis_elegansZK1225.2WBGENE00014236
caenorhabditis_elegansWBGENE00019270
caenorhabditis_elegansWBGENE00019919

Paralogs (8): XYLT2 (ENSG00000015532), XYLT1 (ENSG00000103489), GCNT2 (ENSG00000111846), GCNT7 (ENSG00000124091), GCNT3 (ENSG00000140297), GCNT4 (ENSG00000176928), WSCD1 (ENSG00000179314), GCNT1 (ENSG00000187210)

Protein

Protein identifiers

Sialate:O-sulfotransferase 2 — Q2TBF2 (reviewed: Q2TBF2)

Alternative names: WSC domain-containing protein 2

All UniProt accessions (2): Q2TBF2, F8W030

UniProt curated annotations — full annotation on UniProt →

Function. Sialate:O-sulfotransferase which catalyzes 8-O-sulfation at the Sia-glycan level using 3’-phosphoadenosine 5’-phosphosulfate (PAPS) as a donor, forming 8-O-sulfated Sia (Sia8S)-glycans. Displays selectivity toward glycoproteins such as TF/transferrin.

Subcellular location. Golgi apparatus membrane.

Similarity. Belongs to the WSCD family.

Isoforms (2)

UniProt IDNamesCanonical?
Q2TBF2-11yes
Q2TBF2-22

RefSeq proteins (2): NP_001291376, NP_055468* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR002889WSC_carb-bdDomain
IPR027417P-loop_NTPaseHomologous_superfamily
IPR051589Sialate-O-sulfotransferaseFamily

Pfam: PF01822

UniProt features (12 total): topological domain 2, sequence conflict 2, domain 2, glycosylation site 2, chain 1, transmembrane region 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q2TBF2-F179.000.50

Functional residue map

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

Glycosylation sites (2): 189, 242

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 0 (showing top):

GO Biological Process (0):

GO Molecular Function (1): sulfotransferase activity (GO:0008146)

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

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
transferase activity, transferring sulphur-containing groups1
Golgi apparatus1
bounding membrane of organelle1
cytoplasm1
endomembrane system1
intracellular membrane-bounded organelle1
cellular anatomical structure1

Protein interactions and networks

STRING

1416 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
WSCD2SPATA31A6Q5VVP1435
WSCD2SGSM1Q2NKQ1434
WSCD2ZNF771Q7L3S4397
WSCD2CFAP107Q8N1D5395
WSCD2QSER1Q2KHR3392
WSCD2LRP2BPQ9P2M1388
WSCD2EFCAB12Q6NXP0386
WSCD2LURAP1LQ8IV03380
WSCD2RGS22Q8NE09362
WSCD2ANKHQ9HCJ1352
WSCD2DCAF8L2P0C7V8351
WSCD2SPATA31D1Q6ZQQ2346
WSCD2POC5Q8NA72340
WSCD2FRMD7Q6ZUT3339
WSCD2SCD5Q86SK9327

IntAct

0 interactions, top by confidence:

BioGRID (1): WSCD2 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A8C2LVE3, A2BGL3, F4HXW9, O08889, O17645, O43909, O43916, O93336, O93403, O95461, P25722, P69478, P79948, Q0IIY2, Q2TBF2, Q5NDE4, Q5NDE5, Q5NDE6, Q5NDE7, Q5NDE8, Q5NVB3, Q5R621, Q5RJQ0, Q5XHM7, Q66PG1, Q66PG2, Q66PG3, Q6DBY9, Q6NVP8, Q6P9A2, Q6PA90, Q76EC5, Q76KB1, Q7LFX5, Q7LGA3, Q7LGC8, Q7T3S3, Q800H9, Q8BUB6, Q8CHI9

Diamond homologs: A2BGL3, D4PHA7, P54867, P84675, Q0IIY2, Q16WU7, Q29G54, Q2TBF2, Q505J3, Q5QQ52, Q5QQ53, Q658N2, Q7KVA1, Q7Q297, Q80XH4, Q8K1S7, Q965Q8, Q9VXV9, Q8NCW0, D4AUF1, D4AUF4, Q90Y90, Q924S4, Q96MU8, Q99N43, Q5QQ49, Q5QQ50, Q5QQ51, Q5QQ54, Q5QQ55, Q5QQ56, Q5QQ57, Q811B1, Q86Y38, Q9EPI0, Q9EPI1, Q9EPL0, Q9H1B5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance90
Likely benign1
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

2497 predictions. Top by Δscore:

VariantEffectΔscore
12:108129924:CAG:Cdonor_loss1.0000
12:108129925:AG:Adonor_loss1.0000
12:108129926:GGTAA:Gdonor_loss1.0000
12:108129927:GT:Gdonor_loss1.0000
12:108224728:T:TAacceptor_gain1.0000
12:108224735:TCA:Tacceptor_loss1.0000
12:108224736:CA:Cacceptor_loss1.0000
12:108224737:A:AGacceptor_gain1.0000
12:108224737:AGAT:Aacceptor_gain1.0000
12:108224738:G:GGacceptor_gain1.0000
12:108224738:GAT:Gacceptor_gain1.0000
12:108224738:GATG:Gacceptor_gain1.0000
12:108224857:GAAG:Gdonor_gain1.0000
12:108224859:AGGTG:Adonor_loss1.0000
12:108224860:GG:Gdonor_loss1.0000
12:108224862:T:Adonor_loss1.0000
12:108232893:AAGG:Adonor_loss1.0000
12:108232894:AGGT:Adonor_loss1.0000
12:108232896:G:GAdonor_loss1.0000
12:108232897:T:Adonor_loss1.0000
12:108247986:T:TAacceptor_gain1.0000
12:108247986:TGCAG:Tacceptor_gain1.0000
12:108247988:CA:Cacceptor_loss1.0000
12:108247988:CAG:Cacceptor_gain1.0000
12:108247989:A:ACacceptor_loss1.0000
12:108247989:A:AGacceptor_gain1.0000
12:108247989:AGA:Aacceptor_gain1.0000
12:108247989:AGAGT:Aacceptor_gain1.0000
12:108247990:G:GTacceptor_gain1.0000
12:108247990:GA:Gacceptor_gain1.0000

AlphaMissense

3714 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:108232793:A:CS348R1.000
12:108232795:C:AS348R1.000
12:108232795:C:GS348R1.000
12:108232813:C:AN354K1.000
12:108232813:C:GN354K1.000
12:108240396:G:CK399N1.000
12:108240396:G:TK399N1.000
12:108240402:C:AH401Q1.000
12:108240402:C:GH401Q1.000
12:108240484:T:CF429L1.000
12:108240486:C:AF429L1.000
12:108240486:C:GF429L1.000
12:108240490:C:AR431S1.000
12:108240491:G:CR431P1.000
12:108247993:T:AW450R1.000
12:108247993:T:CW450R1.000
12:108247995:G:CW450C1.000
12:108247995:G:TW450C1.000
12:108248002:T:CF453L1.000
12:108248004:C:AF453L1.000
12:108248004:C:GF453L1.000
12:108206303:T:AC133S0.999
12:108206303:T:CC133R0.999
12:108206304:G:CC133S0.999
12:108206306:T:GY134D0.999
12:108206381:T:AC159S0.999
12:108206381:T:CC159R0.999
12:108206382:G:CC159S0.999
12:108206393:T:AC163S0.999
12:108206393:T:CC163R0.999

dbSNP variants (sampled 300 via entrez): RS1000001833 (12:108205359 A>G), RS1000008605 (12:108247481 G>A,C,T), RS1000012321 (12:108132680 C>T), RS1000080930 (12:108176968 G>C), RS1000098806 (12:108211674 G>A), RS1000124017 (12:108220174 T>A,C), RS1000157544 (12:108138490 G>A,T), RS1000184132 (12:108230242 T>G), RS1000192136 (12:108245589 C>T), RS1000264165 (12:108144630 G>A), RS1000272642 (12:108150262 C>G), RS1000286789 (12:108175509 A>G), RS1000339699 (12:108163330 C>T), RS1000353153 (12:108132405 T>A), RS1000358634 (12:108206797 TGTAG>T)

Disease associations

OMIM: gene MIM:619253 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

28 associations (top):

StudyTraitp-value
GCST001419_5Temperament (bipolar disorder)8.000000e-06
GCST002481_2Acne (severe)5.000000e-06
GCST004015_4Extraversion1.000000e-14
GCST007325_288General risk tolerance (MTAG)2.000000e-17
GCST007483_3Waist-to-hip ratio adjusted for BMI (additive genetic model)1.000000e-09
GCST007487_54Waist-to-hip ratio adjusted for BMI (additive genetic model)9.000000e-09
GCST007492_16Waist-to-hip ratio adjusted for BMI (additive genetic model)9.000000e-07
GCST007494_12Waist-to-hip ratio adjusted for BMI (additive genetic model)8.000000e-06
GCST007515_37Type 2 diabetes3.000000e-08
GCST007516_27Type 2 diabetes (adjusted for BMI)1.000000e-07
GCST007517_19Type 2 diabetes9.000000e-08
GCST007518_25Type 2 diabetes (adjusted for BMI)6.000000e-08
GCST007561_70Sleep duration3.000000e-08
GCST007710_17Anxiety/tension (special factor of neuroticism)2.000000e-10
GCST007847_116Type 2 diabetes1.000000e-08
GCST008103_157Bipolar disorder6.000000e-06
GCST009312_10Antisaccade task score2.000000e-06
GCST009379_344Type 2 diabetes8.000000e-12
GCST010118_84Type 2 diabetes8.000000e-12
GCST010926_2Waist-to-hip ratio adjusted for BMI5.000000e-11
GCST010988_501Adult body size2.000000e-14
GCST90000025_995Appendicular lean mass4.000000e-39
GCST90000026_38Appendicular lean mass7.000000e-19
GCST90000027_18Appendicular lean mass1.000000e-23
GCST90020024_236A body shape index8.000000e-11
GCST90020025_102Waist-to-hip ratio adjusted for BMI5.000000e-09
GCST90020027_1681Waist-hip index6.000000e-09
GCST90020029_465Waist circumference adjusted for body mass index6.000000e-09

EFO canonical traits (8, from GWAS)

EFO IDTrait name
EFO:0004365personality trait
EFO:0004317extraversion
EFO:0008579risk-taking behaviour
EFO:0007788BMI-adjusted waist-hip ratio
EFO:0009863anxiety measurement
EFO:0007969cognitive inhibition measurement
EFO:0004980appendicular lean mass
EFO:0007789BMI-adjusted waist circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

14 total (human), top 14 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, increases expression3
Phenylmercuric Acetateaffects cotreatment, decreases expression2
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression, affects cotreatment, decreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamidedecreases expression, affects cotreatment1
dorsomorphinaffects cotreatment, decreases expression1
Benzo(a)pyreneaffects methylation, increases methylation1
Carbamazepineaffects expression1
Doxorubicinincreases expression1
Folic Aciddecreases expression1
Lipopolysaccharidesincreases expression, affects cotreatment, decreases expression, affects response to substance1
Tobacco Smoke Pollutiondecreases expression1
Triclosandecreases expression1
Aflatoxin B1decreases methylation1
Antirheumatic Agentsincreases expression1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.4
BioBTree
v2.0.2

Sources 74

This page pulls from 74 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomerefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot