Is CDT1 p.Ala55fs (c.162_163insTCCC) pathogenic?

CDT1 p.Ala55fs (c.162163insTCCC) is classified Likely pathogenic in CDT1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-20). Associated with Meier-Gorlin syndrome 4.

What condition is associated with CDT1 p.Ala55fs (c.162_163insTCCC)?

CDT1 p.Ala55fs (c.162_163insTCCC) is associated with Meier-Gorlin syndrome 4 (ClinVar).

CDT1 p.Ala55fs

c.162_163insTCCC · VCV4849302

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

Meier-Gorlin syndrome 4

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 1 of 10
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.35	GERP -1.9

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

Variant & gene context

Gene: CDT1
Protein: p.Ala55fs
Coding: c.162_163insTCCC
MANE Select: NM_030928
Type: Insertion
Location: chr16:88803990 (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 55: the 'disordered' region

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

Disease context

Meier-Gorlin syndrome 4 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CDT1 c.832+1G>A Pathogenic/Likely pathogenic ★★ same condition
CDT1 p.Arg462Gln Pathogenic/Likely pathogenic ★★ ⚠ same condition
CDT1 p.Arg250Cys Uncertain significance ★★ ⚠ same condition
CDT1 p.Gly281Arg Uncertain significance ★★ ⚠ same condition
CDT1 p.Val204Met Uncertain significance ★★ same condition
CDT1 p.Cys234Arg Benign ★★ same condition
CDT1 p.His305= Benign ★★ same condition
CDT1 p.Leu529= Benign ★★ 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/cdt1-p-ala55fs (accessed [today's date]).

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