Is CDC16 p.Ile132= (c.396C>T) pathogenic?

CDC16 p.Ile132= (c.396C>T) is classified Benign in CDC16 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2018-04-16). Common (popmax 8.54%, afr) — too common for a highly-penetrant pathogenic allele.

CDC16 p.Ile132=

Q: How common is CDC16 p.Ile132= (c.396C>T) in the general population?

CDC16 p.Ile132= (c.396C>T) is common (popmax 8.54%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.396C>T · rs17337919 · VCV773720

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Common

common (popmax 8.54%, afr) — too common for a highly-penetrant pathogenic allele

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 1.2	GERP -1.7, phastCons 1
Overall
CADD	8.355	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.54% African / African-American · 6,356/74,424 alleles

Filtering AF 8.36% ClinGen BA1/BS1 input FAF95, joint · FAF99 8.29%

Overall 0.441% 7,078/1,606,358 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	8.54%	12
Remaining individualsnot grpmax-eligible	0.553%	181
Admixed American	0.535%	187
Middle Eastern	0.299%	334
South Asian	0.0101%	9,899
European (non-Finnish)	0.00357%	28,047

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: CDC16
Protein: p.Ile132=
Coding: c.396C>T
MANE Select: NM_001078645
dbSNP: rs17337919
Type: single nucleotide variant
Location: chr13:114242135 (GRCh38)
Gene constraint: LOEUF 0.657 · pLI 0.02 (gnomAD)
Structure: AlphaFold pLDDT 78.89 · 21 PDB
Residue 132: an α-helix

Full CDC16 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CDC16 p.Ile132Val Uncertain significance ★ ⚠ same residue
CDC16 p.Ala142Thr Uncertain significance ★ ⚠ same type
CDC16 p.Ala319Thr Uncertain significance ★ ⚠ same type
CDC16 p.Ala44Gly Uncertain significance ★ ⚠ same type
CDC16 p.Ala479Ser Uncertain significance ★ ⚠ same type
CDC16 p.Ala51Thr Uncertain significance ★ ⚠ same type
CDC16 p.Ala536Ser Uncertain significance ★ ⚠ same type
CDC16 p.Ala57Thr Uncertain significance ★ ⚠ 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/cdc16-p-ile132 (accessed [today's date]).

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