Is CDT1 p.Cys234Pro (c.700_701delinsCC) pathogenic?

CDT1 p.Cys234Pro (c.700701delinsCC) is classified Uncertain significance in CDT1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-12-19). Absent from gnomAD.

How common is CDT1 p.Cys234Pro (c.700_701delinsCC) in the general population?

CDT1 p.Cys234Pro (c.700_701delinsCC) is absent from gnomAD (gnomAD).

CDT1 p.Cys234Pro

c.700_701delinsCC · rs2508204248 · VCV1947447

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 2.2	GERP -1.1, phastCons 0.98
Regional constraint	o/e 1.19	unconstrained · MANE · 4,443 bp · p 1.2e-07 · regional, not allelic

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: CDT1
Protein: p.Cys234Pro
Coding: c.700_701delinsCC
MANE Select: NM_030928
dbSNP: rs2508204248
Type: Indel
Location: chr16:88805737 (GRCh38)
Gene constraint: LOEUF 1.737 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 74.51 · 6 PDB
Residue 234: a UniProt-annotated variant site (in); an α-helix

Full CDT1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CDT1 p.Cys234Arg Benign ★★ same residue
CDT1 p.Cys234Tyr Uncertain significance ★ ⚠ same residue
CDT1 p.Ala56fs Pathogenic ★ same type
CDT1 p.Gln446delinsArgLeuGlu Likely pathogenic ★ same type
CDT1 c.1123-21_1123-20delinsGT Uncertain significance ★ same type
CDT1 p.Arg295Leu Uncertain significance ★ 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/cdt1-p-cys234pro (accessed [today's date]).

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