SLC35C1

Chr 11AR

solute carrier family 35 member C1

Also known as: CDG2C, FUCT1

NCBI Gene: 55343ENSG00000181830UniProt: Q96A29

This gene encodes a GDP-fucose transporter that is found in the Golgi apparatus. Mutations in this gene result in congenital disorder of glycosylation type IIc. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2009]

Primary Disease Associations & Inheritance

Congenital disorder of glycosylation, type IIcMIM #266265
AR
2
Active trials
24
Pathogenic / LP
362
ClinVar variants
3
Pubs (1 yr)
1.2
Missense Z
0.97
LOEUF
Clinical Summary— SLC35C1
🧬
Gene-Disease Validity (ClinGen)
leukocyte adhesion deficiency type II · ARStrong

Strong evidence — appropriate for clinical testing

⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.02) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
24 Pathogenic / Likely Pathogenic· 182 VUS of 362 total submissions
💊
Clinical Trials
2 active or recruiting trials — potential therapeutic options may be available
📖
GeneReview available — SLC35C1
Authoritative clinical overview · Recommended first read
Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
0.97LOEUF
pLI 0.024
Z-score 1.63
OE 0.43 (0.21–0.97)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
1.16Z-score
OE missense 0.78 (0.69–0.89)
172 obs / 220.6 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.43 (0.21–0.97)
0≤0.351.4
Missense OE0.78 (0.69–0.89)
0≤0.61.4
Synonymous OE1.13
0≤1.21.6
LoF obs/exp: 4 / 9.4Missense obs/exp: 172 / 220.6Syn Z: -1.10
DNGOF
DN
0.76top 25%
GOF
0.75top 25%
LOF
0.2189th %ile

This gene has evidence for multiple mechanisms of pathogenicity (dominant-negative and gain-of-function). Both the Badonyi & Marsh prediction and the broader genomic evidence point to dominant-negative as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

DNprediction above median
GOFprediction 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

362 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic20
Likely Pathogenic4
VUS182
Likely Benign120
Benign20
Conflicting16
20
Pathogenic
4
Likely Pathogenic
182
VUS
120
Likely Benign
20
Benign
16
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
3
2
15
0
20
Likely Pathogenic
0
2
2
0
4
VUS
2
132
46
2
182
Likely Benign
0
4
12
104
120
Benign
0
0
20
0
20
Conflicting
—16
Total514095106362

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

View in ClinVar →

SLC35C1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Gene2Phenotype Curations

SLC35C1-related congenital disorder of glycosylation

definitive
ARLoss Of FunctionAbsent Gene Product
Dev. Disorders
G2P ↗

Gene2Phenotype curations · DECIPHER consortium patient cohort (public variants) · deciphergenomics.org

Clinical Literature
Landmark / reviewRecent case evidence
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Defining the mild variant of leukocyte adhesion deficiency type II (SLC35C1-congenital disorder of glycosylation) and response to l-fucose therapy: Insights from two new families and review of the literature.
Tahata S et al.·Am J Med Genet A
2022Review
In vivo evidence for GDP-fucose transport in the absence of transporter SLC35C1 and putative transporter SLC35C2.
Lu L et al.·J Biol Chem
2023
CDG Therapies: From Bench to Bedside.
Brasil S et al.·Int J Mol Sci
2018Review
Genomic testing identifies monogenic causes in patients with very early-onset inflammatory bowel disease: a multicenter survey in an Iranian cohort.
Eslamian G et al.·Clin Exp Immunol
2024Cohort
L-fucose supplementation in a patient with global hypofucosylation and a mono-allelic variant in SLC35C1: Clinical improvement and assessment of biomarkers.
Starosta RT et al.·Mol Genet Metab
2026Case report
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients