Is CTC1 p.Cys596fs (c.1774_1784dup) pathogenic?

CTC1 p.Cys596fs (c.17741784dup) is classified Pathogenic in CTC1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-02-10). Absent from gnomAD; Associated with dyskeratosis congenita.

What condition is associated with CTC1 p.Cys596fs (c.1774_1784dup)?

CTC1 p.Cys596fs (c.1774_1784dup) is associated with dyskeratosis congenita (ClinVar).

How common is CTC1 p.Cys596fs (c.1774_1784dup) in the general population?

CTC1 p.Cys596fs (c.1774_1784dup) is absent from gnomAD (gnomAD).

How is Dyskeratosis congenita inherited?

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

CTC1 p.Cys596fs

c.1774_1784dup · rs2507917271 · VCV2096265

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

dyskeratosis congenita

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 10 of 23
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.9	GERP 0.7, phastCons 0.98

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: CTC1
Protein: p.Cys596fs
Coding: c.1774_1784dup
MANE Select: NM_025099
dbSNP: rs2507917271
Type: Duplication
Location: chr17:8234488 (GRCh38)
Gene constraint: LOEUF 0.776 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 78.01 · 7 PDB
Residue 596: a β-strand

Full CTC1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

dyskeratosis congenita — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Dyskeratosis congenita (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, X-linked recessive
Onset: Adolescent, Adult, Childhood, Infancy, Neonatal
Prevalence: 1-9 / 1 000 000 (Europe)

Similar variants

CTC1 p.Cys596Ser Uncertain significance ★ ⚠ same residue
CTC1 p.Gly398fs Pathogenic/Likely pathogenic ★★ same condition
CTC1 p.His84fs Pathogenic/Likely pathogenic ★★ same condition
CTC1 p.His945fs Pathogenic/Likely pathogenic ★★ same condition
CTC1 p.Leu961fs Pathogenic ★★ same condition
CTC1 p.Lys562Ter Pathogenic/Likely pathogenic ★★ same condition
CTC1 p.Pro999_Glu1000insTer Pathogenic/Likely pathogenic ★★ same condition
CTC1 p.Ala924fs 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/ctc1-p-cys596fs (accessed [today's date]).

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