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…

Primary Disease Associations & Inheritance

Congenital disorder of glycosylation, type IIcMIM #266265

Clinical highlights

Gene–disease validity (ClinGen)

Strong · leukocyte adhesion deficiency type II · AR · ClinGen 2025

Interpreting a novel variant

Loss of function is the curated mechanism (Gene2Phenotype), though the gene is not strongly LoF-constrained in the population — weigh truncating variants against that tolerance.Curated gene-level mechanism — a prior for triage, not a per-variant call.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.97

LOEUF

LOF

Mechanism· G2P

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

Background carrier burden — how many people carry a rare variant somewhere in SLC35C1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 180

455 rare PASS variants

Rare truncating (LoF)

1 in 7,200

42 rare PASS variants

Rare synonymous (reference)

1 in 210

239 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for SLC35C1. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 240	1 in 7,700
South Asian	~43k	1 in 110	1 in 8,600
Remaining (unassigned)	~30k	1 in 120	none seen
European (Finnish)	~27k	1 in 410	1 in 2,600
Admixed American	~22k	1 in 140	none seen
African / African American	~21k	1 in 120	≈ 1 in 9,300
East Asian	~20k	1 in 190	≈ 1 in 4,000
Ashkenazi Jewish	~13k	1 in 1,000	none seen
Middle Eastern	~2,884	1 in 120	none seen

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.