CTNS
Chr 17ARcystinosin, lysosomal cystine transporter
Also known as: CTNS-LSB, PQLC4, SLC66A4
The protein encoded by this gene functions as a seven-transmembrane domain transporter that moves cystine out of lysosomes using the lysosomal membrane's H+ electrochemical gradient. Mutations cause cystinosis, a lysosomal storage disorder with multiple phenotypes including nephropathic, late-onset juvenile/adolescent nephropathic, atypical nephropathic, and ocular nonnephropathic forms, inherited in an autosomal recessive pattern. Loss of cystine transport function leads to pathogenic cystine accumulation within lysosomes.
Definitive — sufficient evidence for diagnostic panels
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Typical tolerance to LoF variation
Tolerant to missense variation
Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.
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
200 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 22 | 1 | 14 | 1 | 38 |
Likely Pathogenic | 24 | 6 | 0 | 0 | 30 |
VUS | 1 | 16 | 52 | 1 | 70 |
Likely Benign | 0 | 0 | 19 | 17 | 36 |
Benign | 0 | 0 | 17 | 0 | 17 |
Conflicting | — | 8 | |||
| Total | 47 | 23 | 102 | 19 | 199 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in 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.
3D Protein StructureAlphaFold
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
Genetic Newborn Screening for Cystinosis and Primary Hyperoxaluria
RECRUITINGCystinosis and Mitochondrial Metabolism
NOT YET RECRUITINGRare Disease Patient Registry & Natural History Study - Coordination of Rare Diseases at Sanford
RECRUITINGA Long-Term Follow-Up Study of Participants With Cystinosis Who Previously Received CTNS-RD-04
ENROLLING BY INVITATIONDFT383 in Pediatric Participants With Nephropathic Cystinosis
RECRUITINGEuropean Cystinosis Cohort
RECRUITINGExternal Resources
Links to major genomics databases and tools