Is CTNS p.Gly110Val (c.329G>T) pathogenic?

CTNS p.Gly110Val (c.329G>T) is classified Pathogenic in CTNS (ClinVar, No assertion criteria, 1 submitter; last evaluated 2002-12-01). AlphaMissense: likely benign (0.1109); Absent from gnomAD v4.1; Associated with Cystinosis, atypical nephropathic.

What condition is associated with CTNS p.Gly110Val (c.329G>T)?

CTNS p.Gly110Val (c.329G>T) is associated with Cystinosis, atypical nephropathic (ClinVar).

How common is CTNS p.Gly110Val (c.329G>T) in the general population?

CTNS p.Gly110Val (c.329G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CTNS p.Gly110Val (c.329G>T)?

AlphaMissense predicts likely benign (score 0.1109) — an in-silico prediction, not a clinical call.

CTNS p.Gly110Val

c.329G>T · rs121908129 · VCV4457

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1109 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Cystinosis, atypical nephropathic

Computational evidence

Protein change
AlphaMissense	0.1109	likely benign ⚠ discordant with ClinVar
REVEL	0.407	indeterminate
SaProt	LLR -8.59	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	Δ0.89	donor loss · deltas
Pangolin	Δ0.68	loss · gain 0.03 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 9.7	GERP 1.9, phastCons 1
Regional constraint	o/e 0.96	unconstrained · MANE · 20 kb · p 0.4 · regional, not allelic
Overall
CADD	26.1	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CTNS
Protein: p.Gly110Val
Coding: c.329G>T
MANE Select: NM_004937
dbSNP: rs121908129
Type: single nucleotide variant
Location: chr17:3655101 (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 110: a UniProt-annotated variant site (in ctns; atypical; does not affect cystine transport)

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

Disease context

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

Similar variants

CTNS p.Gly110Ser Uncertain significance ★★ ⚠ same residue
CTNS p.Gly110Ala Likely pathogenic ★ ⚠ same residue
CTNS c.140+1G>C Likely pathogenic ★★ same type
CTNS c.140+1G>T Pathogenic/Likely pathogenic ★★ same type
CTNS c.140+2T>C Pathogenic/Likely pathogenic ★★ same type
CTNS c.141-1G>A Pathogenic/Likely pathogenic ★★ same type
CTNS c.141-24T>C Pathogenic ★★ same type
CTNS c.225+3A>T Pathogenic/Likely pathogenic ★★ same type

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-gly110val (accessed [today's date]).

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