WSCD1

Summary

WSCD1 (WSC domain sialate O sulfotransferase 1, HGNC:29060) is a protein-coding gene on chromosome 17p13.2, encoding Sialate:O-sulfotransferase 1 (Q658N2). 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 23302 — RefSeq curated summary.

At a glance

• GWAS associations: 13
• Clinical variants (ClinVar): 144 total
• MANE Select transcript: NM_015253

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29060
Approved symbol	WSCD1
Name	WSC domain sialate O sulfotransferase 1
Location	17p13.2
Locus type	gene with protein product
Status	Approved
Aliases	KIAA0523
Ensembl gene	ENSG00000179314
Ensembl biotype	protein_coding
OMIM	619584
Entrez	23302

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 16 protein_coding, 2 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined

ENST00000317744, ENST00000571494, ENST00000571973, ENST00000572764, ENST00000573634, ENST00000574232, ENST00000574946, ENST00000576233, ENST00000576947, ENST00000714059, ENST00000714060, ENST00000851806, ENST00000851807, ENST00000851808, ENST00000851809, ENST00000851810, ENST00000920364, ENST00000920365, ENST00000920366, ENST00000970109

RefSeq mRNA: 6 — MANE Select: NM_015253 NM_001388405, NM_001388406, NM_001388407, NM_001388408, NM_001388409, NM_015253

CCDS: CCDS32538

Canonical transcript exons

ENST00000317744 — 9 exons

Exon	Start	End
ENSE00001257443	6070379	6070652
ENSE00001303864	6080371	6081085
ENSE00002662846	6120309	6124427
ENSE00003464973	6095102	6095223
ENSE00003514445	6110771	6110935
ENSE00003579418	6109607	6109766
ENSE00003607272	6090321	6090505
ENSE00003608360	6117988	6118188
ENSE00003784786	6087990	6088104

Expression profiles

Bgee: expression breadth ubiquitous, 207 present calls, max score 97.21.

FANTOM5 (CAGE): breadth broad, TPM avg 2.0825 / max 66.3278, expressed in 475 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
159043	0.8677	350
159042	0.7704	329
159044	0.1826	99
159045	0.1499	63
208041	0.0997	65
159046	0.0123	6

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ventricular zone	UBERON:0003053	97.21	gold quality
ganglionic eminence	UBERON:0004023	94.07	gold quality
inferior vagus X ganglion	UBERON:0005363	90.53	gold quality
medial globus pallidus	UBERON:0002477	88.83	gold quality
paraflocculus	UBERON:0005351	88.63	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	87.96	gold quality
cerebellar vermis	UBERON:0004720	86.89	gold quality
medulla oblongata	UBERON:0001896	86.72	gold quality
right hemisphere of cerebellum	UBERON:0014890	86.65	gold quality
cerebellum	UBERON:0002037	86.51	gold quality
cerebellar cortex	UBERON:0002129	86.41	gold quality
cerebellar hemisphere	UBERON:0002245	86.41	gold quality
inferior olivary complex	UBERON:0002127	86.34	gold quality
embryo	UBERON:0000922	86.28	gold quality
globus pallidus	UBERON:0001875	86.14	gold quality
endothelial cell	CL:0000115	86.04	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	85.74	gold quality
spinal cord	UBERON:0002240	85.44	gold quality
subthalamic nucleus	UBERON:0001906	85.26	gold quality
superior vestibular nucleus	UBERON:0007227	85.25	gold quality
corpus callosum	UBERON:0002336	85.17	gold quality
ventral tegmental area	UBERON:0002691	85.06	gold quality
mucosa of transverse colon	UBERON:0004991	84.02	gold quality
midbrain	UBERON:0001891	83.63	gold quality
substantia nigra	UBERON:0002038	83.51	gold quality
amygdala	UBERON:0001876	83.40	gold quality
hindlimb stylopod muscle	UBERON:0004252	83.25	gold quality
dorsal plus ventral thalamus	UBERON:0001897	82.91	gold quality
hypothalamus	UBERON:0001898	82.56	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.55	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-CURD-10	no	92.60
E-ANND-3	no	3.52

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

83 targeting WSCD1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-10401-5P	99.99	65.79	948
HSA-MIR-6793-5P	99.97	65.95	758
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-4302	99.89	67.94	1187
HSA-MIR-3919	99.87	69.45	2489
HSA-MIR-221-5P	99.86	65.45	1052
HSA-MIR-8073	99.86	65.21	1118
HSA-MIR-4779	99.86	66.50	1583
HSA-MIR-629-3P	99.85	67.99	1875
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-6875-3P	99.82	70.26	2983
HSA-MIR-6739-5P	99.80	67.87	2806
HSA-MIR-4668-5P	99.79	70.58	3782
HSA-MIR-4713-5P	99.78	67.80	1794
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-6764-5P	99.75	67.89	2304
HSA-MIR-6733-5P	99.74	67.94	2759
HSA-MIR-24-3P	99.59	69.97	1934
HSA-MIR-1915-3P	99.58	66.79	1988
HSA-MIR-18A-3P	99.56	65.68	1092
HSA-MIR-3153	99.55	67.59	2337
HSA-MIR-4753-5P	99.54	68.51	1356

Cross-species orthologs

19 orthologs

Organism	Symbol	Gene ID
danio_rerio	wscd1b	ENSDARG00000078006
danio_rerio	WSCD1	ENSDARG00000098113
mus_musculus	Wscd1	ENSMUSG00000020811
rattus_norvegicus	Wscd1	ENSRNOG00000007869
caenorhabditis_elegans	gly-16	WBGENE00001641
caenorhabditis_elegans	gly-17	WBGENE00001642
caenorhabditis_elegans	gly-18	WBGENE00001643
caenorhabditis_elegans	gly-19	WBGENE00001644
caenorhabditis_elegans		WBGENE00009148
caenorhabditis_elegans	F30A10.4	WBGENE00009263
caenorhabditis_elegans		WBGENE00011090
caenorhabditis_elegans	T09E11.6	WBGENE00011655
caenorhabditis_elegans	T09E11.9	WBGENE00011658
caenorhabditis_elegans	T27F6.1	WBGENE00012102
caenorhabditis_elegans		WBGENE00012135
caenorhabditis_elegans		WBGENE00013119
caenorhabditis_elegans	ZK1225.2	WBGENE00014236
caenorhabditis_elegans		WBGENE00019270
caenorhabditis_elegans		WBGENE00019919

Paralogs (8): XYLT2 (ENSG00000015532), WSCD2 (ENSG00000075035), XYLT1 (ENSG00000103489), GCNT2 (ENSG00000111846), GCNT7 (ENSG00000124091), GCNT3 (ENSG00000140297), GCNT4 (ENSG00000176928), GCNT1 (ENSG00000187210)

Protein

Protein identifiers

Sialate:O-sulfotransferase 1 — Q658N2 (reviewed: Q658N2)

Alternative names: WSC domain-containing protein 1

All UniProt accessions (6): A0A1B0GXC0, A0AAQ5BHC8, Q658N2, I3L0U0, I3L127, I3L3E6

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 glycolipids such as GM1 gangliosides.

Subcellular location. Golgi apparatus membrane.

Similarity. Belongs to the WSCD family.

RefSeq proteins (6): NP_001375334, NP_001375335, NP_001375336, NP_001375337, NP_001375338, NP_056068* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000863	Sulfotransferase_dom	Domain
IPR002889	WSC_carb-bd	Domain
IPR027417	P-loop_NTPase	Homologous_superfamily
IPR051589	Sialate-O-sulfotransferase	Family

Pfam: PF00685, PF01822

Catalyzed reactions (Rhea), 1 shown:

• a ganglioside GM1b + 3’-phosphoadenylyl sulfate = an 8-O-sulfo-ganglioside GM1b + adenosine 3’,5’-bisphosphate + H(+) (RHEA:74843)

UniProt features (9 total): topological domain 2, domain 2, glycosylation site 2, chain 1, transmembrane region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q658N2-F1	77.87	0.44

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): 257, 348

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 74 (showing top): BENPORATH_ES_WITH_H3K27ME3, BROWNE_HCMV_INFECTION_48HR_DN, SABATES_COLORECTAL_ADENOMA_DN, GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS, BARRIER_CANCER_RELAPSE_TUMOR_SAMPLE_DN, LEIN_OLIGODENDROCYTE_MARKERS, GRYDER_PAX3FOXO1_TOP_ENHANCERS, RAY_TUMORIGENESIS_BY_ERBB2_CDC25A_UP, MIKKELSEN_MCV6_HCP_WITH_H3K27ME3, GOMF_TRANSFERASE_ACTIVITY_TRANSFERRING_SULPHUR_CONTAINING_GROUPS, DAVICIONI_MOLECULAR_ARMS_VS_ERMS_UP, MIKKELSEN_MEF_HCP_WITH_H3K27ME3, MARTENS_TRETINOIN_RESPONSE_UP, VERHAAK_GLIOBLASTOMA_CLASSICAL, CHEMNITZ_RESPONSE_TO_PROSTAGLANDIN_E2_DN

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:

Category	Terms
transferase activity, transferring sulphur-containing groups	1
Golgi apparatus	1
bounding membrane of organelle	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

898 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
WSCD1	RNF175	Q8N4F7	479
WSCD1	KLHDC8A	Q8IYD2	431
WSCD1	SYNDIG1	Q9H7V2	430
WSCD1	TMC5	Q6UXY8	419
WSCD1	AKR1E2	Q96JD6	414
WSCD1	MANEA	Q5SRI9	399
WSCD1	SLC37A1	P57057	398
WSCD1	TRERF1	Q96PN7	394
WSCD1	SDF2	Q99470	393
WSCD1	KCNAB3	O43448	385
WSCD1	SEZ6	Q53EL9	382
WSCD1	MYCBPAP	Q8TBZ2	381
WSCD1	IGSF21	Q96ID5	379
WSCD1	LINGO2	Q7L985	379
WSCD1	PKDCC	Q504Y2	377

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A0D3QS98, A0A0D3QS99, A2A5I3, O19010, O19011, O42596, P01137, P04202, P04629, P07200, P09533, P16562, P17246, P18341, P35739, P50414, P54108, P54831, P57110, Q01974, Q38HS2, Q3KPV7, Q3UFB7, Q505J3, Q5R7Y0, Q5T4F7, Q60477, Q658N2, Q6UWX4, Q7T141, Q7TSQ1, Q80XH4, Q8BG58, Q91009, Q99JR5, Q9CXM0, Q9D2G9, Q9EQT5, Q9GZM7, Q9H3Y0

Diamond homologs: A2BGL3, D4PHA7, P54867, P84675, Q0IIY2, Q16WU7, Q29G54, Q2TBF2, Q505J3, Q5QQ52, Q5QQ53, Q658N2, Q7KVA1, Q7Q297, Q80XH4, Q8K1S7, Q965Q8, Q9VXV9, A2YPX3, D4AUF4, Q0D3N0, Q8GY91, Q8NCW0, Q924S4, Q96MU8, Q99N43, Q9FLC0, D4AUF1, Q90Y90, Q5QQ49, Q5QQ50, Q5QQ51, Q5QQ54, Q5QQ55, Q5QQ56, Q5QQ57, Q811B1, Q86Y38, Q9EPI0, Q9EPI1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	131
Likely benign	8
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1969 predictions. Top by Δscore:

Variant	Effect	Δscore
17:6087988:A:AG	acceptor_gain	1.0000
17:6087989:G:GG	acceptor_gain	1.0000
17:6088100:GAGCG:G	donor_gain	1.0000
17:6088101:AGCGG:A	donor_loss	1.0000
17:6088102:GCG:G	donor_gain	1.0000
17:6088102:GCGGT:G	donor_loss	1.0000
17:6088103:CGGTG:C	donor_loss	1.0000
17:6088105:G:GG	donor_gain	1.0000
17:6088105:GTG:G	donor_loss	1.0000
17:6088106:TGAGT:T	donor_loss	1.0000
17:6088107:GAGT:G	donor_loss	1.0000
17:6090315:CTGCA:C	acceptor_loss	1.0000
17:6090316:TGCA:T	acceptor_loss	1.0000
17:6090317:GCAG:G	acceptor_loss	1.0000
17:6090318:CAGGT:C	acceptor_loss	1.0000
17:6090319:A:AG	acceptor_gain	1.0000
17:6090319:A:AT	acceptor_loss	1.0000
17:6090320:G:GG	acceptor_gain	1.0000
17:6090501:G:GT	donor_gain	1.0000
17:6090501:GAAGC:G	donor_gain	1.0000
17:6090504:GC:G	donor_gain	1.0000
17:6090506:G:GG	donor_gain	1.0000
17:6095220:GAAA:G	donor_gain	1.0000
17:6095224:G:GG	donor_gain	1.0000
17:6117986:A:AG	acceptor_gain	1.0000
17:6117986:AG:A	acceptor_gain	1.0000
17:6117987:G:GG	acceptor_gain	1.0000
17:6117987:GG:G	acceptor_gain	1.0000
17:6118186:AAGG:A	donor_loss	1.0000
17:6118188:GG:G	donor_loss	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000020614 (17:6092753 G>A), RS1000032252 (17:6086542 C>T), RS1000168980 (17:6114005 A>C), RS1000175510 (17:6107976 C>T), RS1000251644 (17:6087862 C>T), RS1000287459 (17:6114466 G>T), RS1000288368 (17:6082845 G>A), RS1000351588 (17:6102913 T>C), RS1000413863 (17:6108130 C>G,T), RS1000423853 (17:6082580 G>A), RS1000628662 (17:6079210 C>T), RS1000693759 (17:6084103 C>T), RS1000874854 (17:6097579 C>T), RS1000899886 (17:6079381 G>A), RS1000972699 (17:6073608 C>T)

Disease associations

OMIM: gene MIM:619584 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

13 associations (top):

Study	Trait	p-value
GCST002160_4	Wegener’s granulomatosis	2.000000e-07
GCST002541_111	Menarche (age at onset)	2.000000e-08
GCST002932_2	Manganese levels	5.000000e-06
GCST003075_57	Cognitive decline rate in late mild cognitive impairment	8.000000e-07
GCST003075_76	Cognitive decline rate in late mild cognitive impairment	1.000000e-06
GCST003720_43	Migraine	7.000000e-09
GCST006012_1	C-reactive protein levels	2.000000e-09
GCST006193_6	Diastolic blood pressure x smoking status (current vs non-current) interaction (2df test)	2.000000e-10
GCST006194_8	Diastolic blood pressure x smoking status (current vs non-current) interaction (1df test)	2.000000e-08
GCST006304_14	Irritable bowel syndrome	3.000000e-06
GCST007202_5	High density lipoprotein cholesterol levels	3.000000e-06
GCST008761_6	Sucrose liking	7.000000e-06
GCST011350_5	C-reactive protein levels	3.000000e-08

EFO canonical traits (7, from GWAS)

EFO ID	Trait name
EFO:0004703	age at menarche
EFO:0007710	cognitive decline measurement
EFO:0004458	C-reactive protein measurement
EFO:0006336	diastolic blood pressure
EFO:0006527	smoking status measurement
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0010157	sucrose liking measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

34 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases expression, affects cotreatment, decreases expression, affects expression	7
trichostatin A	affects cotreatment, decreases expression, increases expression	3
bisphenol A	decreases expression, increases methylation	2
Benzo(a)pyrene	affects methylation	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
p-Chloromercuribenzoic Acid	affects cotreatment, decreases expression	2
aristolochic acid I	increases expression	1
fluorene-9-bisphenol	increases expression	1
methylmercuric chloride	decreases expression	1
propionaldehyde	increases expression	1
sodium arsenite	increases expression	1
butyraldehyde	increases expression	1
pentanal	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	decreases expression	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Zoledronic Acid	decreases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Aldehydes	increases expression	1
Cadmium	increases expression	1
Diethylhexyl Phthalate	decreases expression	1
Phthalic Acids	increases methylation	1
Plant Extracts	affects cotreatment, decreases expression	1
Rotenone	increases expression	1
Testosterone	increases expression	1
Tetrachlorodibenzodioxin	affects cotreatment, increases expression	1
Vitamin E	decreases expression	1

Clinical trials (associated diseases)

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