Is CDC27 p.Thr409= (c.1227A>C) pathogenic?

CDC27 p.Thr409= (c.1227A>C) is classified Likely benign in CDC27 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-04-01). Absent from gnomAD v4.1.

How common is CDC27 p.Thr409= (c.1227A>C) in the general population?

CDC27 p.Thr409= (c.1227A>C) is absent from gnomAD v4.1 (gnomAD).

CDC27 p.Thr409=

c.1227A>C · VCV4820767

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.6	GERP -0.75, phastCons 1
Overall
CADD	9.212	PHRED · no single calibrated threshold — expert panels disagree

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: CDC27
Protein: p.Thr409=
Coding: c.1227A>C
MANE Select: NM_001256
Type: single nucleotide variant
Location: chr17:47142380 (GRCh38)
Gene constraint: LOEUF 0.38 · pLI 0.96 (gnomAD)
Structure: AlphaFold pLDDT 70.02 · 25 PDB
Residue 409: the 'disordered' region

Full CDC27 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CDC27 p.Pro286= Benign/Likely benign ★★ same type
CDC27 c.27+2T>C Uncertain significance ★ same type
CDC27 p.Ala586= Likely benign ★ same type
CDC27 p.Leu173= Likely benign ★ same type
CDC27 p.Pro421= Likely benign ★ same type
CDC27 p.Thr167= Likely benign ★ same type
CDC27 p.Thr171= Likely benign ★ same type
CDC27 p.Thr446= Likely benign ★ 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/cdc27-p-thr409 (accessed [today's date]).

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