SLC35C1

Chr 11AR

solute carrier family 35 member C1

Also known as: CDG2C, FUCT1

NCBI Gene: 55343 ENSG00000181830 UniProt: Q96A29 OMIM: 605881

The protein functions as a GDP-fucose transporter in the Golgi apparatus, importing GDP-fucose from the cytoplasm into the Golgi lumen in exchange for GMP. Mutations cause congenital disorder of glycosylation type IIc, which follows autosomal recessive inheritance. This condition affects protein glycosylation and typically presents in infancy with developmental delays, seizures, and other multisystem manifestations.

OMIM ResearchSummary from RefSeq, OMIM, UniProt

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]

OMIM ResearchGenerating clinical summary…

LOFmechanismARLOEUF 0.971 OMIM phenotype

Clinical Summary— SLC35C1

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Gene-Disease Validity (ClinGen)

leukocyte adhesion deficiency type II · ARStrong

Strong evidence — appropriate for clinical testing

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Population Constraint (gnomAD)

Low constraint (pLI 0.02) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

10 unique Pathogenic / Likely Pathogenic· 176 VUS of 346 total submissions

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Clinical Trials

2 active or recruiting trials — potential therapeutic options may be available

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?

0.97LOEUF

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 OE?0.43 (0.21–0.97)

0≤0.351.4

Missense OE?0.78 (0.69–0.89)

0≤0.61.4

Synonymous OE?1.13

0≤1.21.6

LoF obs/exp: 4 / 9.4Missense obs/exp: 172 / 220.6Syn Z: -1.10

Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗

definitiveSLC35C1-related congenital disorder of glycosylationLOFAR

This gene — mechanism propensity

Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.

0.76top 25%

GOF

0.75top 25%

LOF

0.2189th %ile

The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.

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

ClinVar Variant Classifications

346 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic7

Likely Pathogenic3

VUS176

Likely Benign119

Benign20

Conflicting17

Pathogenic

Likely Pathogenic

176

VUS

119

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	5	2	0	0	7
Likely Pathogenic	1	2	0	0	3
VUS	2	136	37	1	176
Likely Benign	0	3	12	104	119
Benign	0	0	20	0	20
Conflicting	—				17
Total	8	143	69	105	342

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

View in ClinVar →

15 pathogenic / likely-pathogenic (of 23) ClinVar copy-number / structural variants overlap SLC35C1 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →