Is CCDC32 p.Val76= (c.228G>A) pathogenic?

CCDC32 p.Val76= (c.228G>A) is classified Likely benign in CCDC32 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-02-01). Ultra-rare (popmax 0.0533%, amr).

How common is CCDC32 p.Val76= (c.228G>A) in the general population?

CCDC32 p.Val76= (c.228G>A) is ultra-rare (popmax 0.0533%, amr) (gnomAD).

CCDC32 p.Val76=

c.228G>A · VCV4822201

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0533%, amr)

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 -2.2	GERP -0.59
Overall
CADD	7.188	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0533% Admixed American · 32/59,986 alleles

Filtering AF 0.0388% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0339%

Overall 0.00198% 32/1,613,840 alleles · ultra-rare exomes 31/1,461,648 · genomes 1/152,192 · joint denominator

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: CCDC32
Protein: p.Val76=
Coding: c.228G>A
MANE Select: NM_001080792
Type: single nucleotide variant
Location: chr15:40562788 (GRCh38)
Gene constraint: LOEUF 0.76 · pLI 0.19 (gnomAD)
Structure: AlphaFold pLDDT 69.74

Full CCDC32 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CCDC32 c.-13+196A>T Uncertain significance ★ same type
CCDC32 p.Asp45His Uncertain significance ★ ⚠ same type
CCDC32 p.Gly177Arg Uncertain significance ★ ⚠ same type
CCDC32 p.Tyr157Ter Uncertain significance ★ same type
CCDC32 c.402-6939A>C Likely benign ★ same type
CCDC32 c.-13+210T>C Likely benign ★ same type
CCDC32 p.Asp172= Likely benign ★ same type
CCDC32 p.Ser6= 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/ccdc32-p-val76 (accessed [today's date]).

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