Is CTNS p.Val348del (c.1039GTC[1]) pathogenic?

CTNS p.Val348del (c.1039GTC[1]) is classified Uncertain significance in CTNS (ClinVar, No assertion criteria, 1 submitter; last evaluated 2017-01-10). Absent from gnomAD; Associated with nephropathic cystinosis.

What condition is associated with CTNS p.Val348del (c.1039GTC[1])?

CTNS p.Val348del (c.1039GTC[1]) is associated with nephropathic cystinosis (ClinVar).

How common is CTNS p.Val348del (c.1039GTC[1]) in the general population?

CTNS p.Val348del (c.1039GTC[1]) is absent from gnomAD (gnomAD).

How is Cystinosis inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

CTNS p.Val348del

c.1039GTC[1] · rs1555564879 · VCV550343

Uncertain significance No assertion criteria

Classification

Uncertain significance

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

nephropathic cystinosis

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 1.6, phastCons 1

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CTNS
Protein: p.Val348del
Coding: c.1039GTC[1]
MANE Select: NM_004937
dbSNP: rs1555564879
Type: Microsatellite
Location: chr17:3660303 (GRCh38)
Gene constraint: LOEUF 0.754 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 89.27 · 6 PDB
Residue 348: an α-helix; a UniProt-annotated variant site (in ctns; partial relocation to the cell membrane; abolished cystine transport)

Full CTNS gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

nephropathic cystinosis — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Cystinosis (Orphanet):

Inheritance: Autosomal recessive
Onset: Adolescent, Adult, Childhood, Infancy
Prevalence: 1-9 / 1 000 000 (Worldwide)

Similar variants

CTNS p.Val348Ile Uncertain significance ★★ ⚠ same residue
CTNS c.225+5_225+8del Likely pathogenic ★★ same condition
CTNS p.Asp205del Pathogenic ★★ same condition
CTNS p.Ser234fs Pathogenic ★★ same condition
CTNS p.Ser86fs Pathogenic ★ same condition
CTNS p.Phe208del Uncertain significance ★ same condition
CTNS p.Phe350del Uncertain significance ★ same condition
CTNS p.Cys20_Glu21delinsTer Pathogenic same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/ctns-p-val348del (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown