Is CDC27 p.Tyr58= (c.174T>C) pathogenic?

CDC27 p.Tyr58= (c.174T>C) is classified Likely benign in CDC27 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-01). Very rare (popmax 0.00134%, afr).

How common is CDC27 p.Tyr58= (c.174T>C) in the general population?

CDC27 p.Tyr58= (c.174T>C) is very rare (popmax 0.00134%, afr) (gnomAD).

CDC27 p.Tyr58=

c.174T>C · VCV3770772

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00134%, afr)

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 3	GERP -0.88, phastCons 1
Overall
CADD	10.85	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00134% African / African-American · 1/74,670 alleles

Overall 0.000138% 2/1,448,406 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00134%	74,670
South Asian	0.00113%	88,658

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: CDC27
Protein: p.Tyr58=
Coding: c.174T>C
MANE Select: NM_001256
Type: single nucleotide variant
Location: chr17:47171994 (GRCh38)
Gene constraint: LOEUF 0.38 · pLI 0.96 (gnomAD)
Structure: AlphaFold pLDDT 70.02 · 25 PDB
Residue 58: an α-helix

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.Thr409= 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-tyr58 (accessed [today's date]).

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