WSCD1

Chr 17

WSC domain sialate O sulfotransferase 1

NCBI Gene: 23302 ENSG00000179314 UniProt: Q658N2 OMIM: 619584

WSCD1 encodes a sialate:O-sulfotransferase that catalyzes 8-O-sulfation of sialic acid residues on glycolipids including GM1 gangliosides, functioning at the Golgi membrane. The gene is highly constrained against loss-of-function variants (pLI near 1.0), suggesting that mutations would likely cause severe developmental disorders. However, no specific human disease phenotypes have been definitively associated with WSCD1 mutations to date.

OMIM ResearchSummary from RefSeq, UniProt

Predicted to enable sulfotransferase activity. Predicted to be located in Golgi membrane. [provided by Alliance of Genome Resources, Jul 2025]

OMIM ResearchGenerating clinical summary…

DNmechanismLOEUF 0.68

Clinical Summary— WSCD1

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

129 VUS of 141 total submissions

Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.68LOEUF

pLI 0.000

Z-score 2.88

OE 0.42 (0.27–0.68)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.54Z-score

OE missense 0.92 (0.84–1.01)

359 obs / 389.2 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.42 (0.27–0.68)

0≤0.351.4

Missense OE?0.92 (0.84–1.01)

0≤0.61.4

Synonymous OE?1.13

0≤1.21.6

LoF obs/exp: 12 / 28.6Missense obs/exp: 359 / 389.2Syn Z: -1.28

This gene — mechanism propensity

0.6454th %ile

GOF

0.5954th %ile

LOF

0.3163th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

141 submitted variants in ClinVar

ClinVar

Classification Summary

VUS129

Likely Benign7

129

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	0	0	0	0
Likely Pathogenic	0	0	0	0
VUS	129	0	0	129
Likely Benign	4	1	2	7
Benign	0	0	0	0
Total	133	1	2	136

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

19 pathogenic / likely-pathogenic (of 27) ClinVar copy-number / structural variants overlap WSCD1 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →