CTNS

Chr 17

cystinosin, lysosomal cystine transporter

Also known as: CTNS-LSB, PQLC4, SLC66A4

NCBI Gene: 1497ENSG00000040531UniProt: O60931

This gene encodes a seven-transmembrane domain protein that functions to transport cystine out of lysosomes. Its activity is driven by the H+ electrochemical gradient of the lysosomal membrane. Mutations in this gene cause cystinosis, a lysosomal storage disorder. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2009]

GeneReviewsResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtCystinosis, nephropathic type
UniProtCystinosis, adult, non-nephropathic type
UniProtCystinosis, late-onset juvenile or adolescent nephropathic type

Clinical highlights

Gene-disease validity (ClinGen)
cystinosis · ARDefinitivesufficient evidence for diagnostic panels
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.
5
Active trials
57
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.80
LOEUF
LOF
Mechanism· G2P
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GeneReview available — CTNS
Authoritative clinical overview · Recommended first read
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Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?
0.80LOEUF
pLI 0.000
Z-score 2.23
OE 0.46 (0.28–0.80)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?
-0.92Z-score
OE missense 1.17 (1.06–1.29)
271 obs / 231.7 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?
LoF OE?0.46 (0.28–0.80)
0≤0.351.4
Missense OE?1.17 (1.06–1.29)
0≤0.61.4
Synonymous OE?1.23
0≤1.21.6
LoF obs/exp: 9 / 19.7Missense obs/exp: 271 / 231.7Syn Z: -1.77

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

CTNS · protein map & ClinVar variants

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

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