Is CDC27 p.Leu173= (c.517T>C) pathogenic?

CDC27 p.Leu173= (c.517T>C) is classified Likely benign in CDC27 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-06-01). Very rare (popmax 8.48e-05%, nfe).

How common is CDC27 p.Leu173= (c.517T>C) in the general population?

CDC27 p.Leu173= (c.517T>C) is very rare (popmax 8.48e-05%, nfe) (gnomAD).

CDC27 p.Leu173=

c.517T>C · VCV3777815

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 8.48e-05%, nfe)

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 0.28, phastCons 1
Overall
CADD	8.353	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.48e-05% European (non-Finnish) · 1/1,179,800 alleles

Overall 6.84e-05% 1/1,461,518 alleles · very rare

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.Leu173=
Coding: c.517T>C
MANE Select: NM_001256
Type: single nucleotide variant
Location: chr17:47157343 (GRCh38)
Gene constraint: LOEUF 0.38 · pLI 0.96 (gnomAD)
Structure: AlphaFold pLDDT 70.02 · 25 PDB

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.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
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-leu173 (accessed [today's date]).

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