Is CTNS p.Val31fs (c.91dup) pathogenic?

CTNS p.Val31fs (c.91dup) is classified Pathogenic in CTNS (ClinVar, No assertion criteria, 1 submitter). Absent from gnomAD; Associated with cystinosis.

What condition is associated with CTNS p.Val31fs (c.91dup)?

CTNS p.Val31fs (c.91dup) is associated with cystinosis (ClinVar).

How common is CTNS p.Val31fs (c.91dup) in the general population?

CTNS p.Val31fs (c.91dup) 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.Val31fs

c.91dup · rs879255613 · VCV253208

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

cystinosis

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 4 of 12
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -3.1	GERP -3.1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

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.Val31fs
Coding: c.91dup
MANE Select: NM_004937
dbSNP: rs879255613
Type: Duplication
Location: chr17:3647472 (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 31: a β-strand

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

Disease context

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.Ser310fs Pathogenic ★★ same condition
CTNS p.Thr277fs Pathogenic ★★ same condition
CTNS p.Val233fs Pathogenic ★★ same condition
CTNS p.Trp245fs Likely pathogenic ★ same condition
CTNS p.Tyr143fs Likely pathogenic ★ same condition
CTNS p.Val31= Likely benign ★ same residue
CTNS c.140+2T>C Pathogenic/Likely pathogenic ★★ same condition
CTNS c.225+3A>T Pathogenic/Likely 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-val31fs (accessed [today's date]).

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