Is CDT1 p.Leu292Arg (c.875T>G) pathogenic?

CDT1 p.Leu292Arg (c.875T>G) is classified Uncertain significance in CDT1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-04-08). AlphaMissense: ambiguous (0.3734); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with CDT1 p.Leu292Arg (c.875T>G)?

CDT1 p.Leu292Arg (c.875T>G) is associated with Inborn genetic diseases (ClinVar).

How common is CDT1 p.Leu292Arg (c.875T>G) in the general population?

CDT1 p.Leu292Arg (c.875T>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CDT1 p.Leu292Arg (c.875T>G)?

AlphaMissense predicts ambiguous (score 0.3734) — an in-silico prediction, not a clinical call.

CDT1 p.Leu292Arg

c.875T>G · VCV3265624

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3734 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.3734	ambiguous
REVEL	0.361	indeterminate
SaProt	LLR -11.86	damaging
Splicing
SpliceAI	Δ0.42	acceptor loss, 5 bp away · masked 0 · deltas
Constraint at this position
Conservation	phyloP 7.9	GERP 1.4, phastCons 1
Regional constraint	o/e 1.19	unconstrained · MANE · 4,443 bp · p 1.2e-07 · regional, not allelic
Overall
CADD	24.3	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: CDT1
Protein: p.Leu292Arg
Coding: c.875T>G
MANE Select: NM_030928
Type: single nucleotide variant
Location: chr16:88806063 (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 292: an α-helix

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CDT1 p.Leu292= Likely benign ★ same residue
CDT1 p.Ala11Val Uncertain significance ★★ ⚠ same condition
CDT1 p.Ala144Ser Uncertain significance ★★ ⚠ same condition
CDT1 p.Ala167Thr Uncertain significance ★★ ⚠ same condition
CDT1 p.Ala217Val Uncertain significance ★★ ⚠ same condition
CDT1 p.Ala414Ser Uncertain significance ★★ ⚠ same condition
CDT1 p.Ala431Thr Uncertain significance ★★ ⚠ same condition
CDT1 p.Ala534Val Uncertain significance ★★ ⚠ 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-leu292arg (accessed [today's date]).

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