Is CCDC69 p.Ile192Val (c.574A>G) pathogenic?

CCDC69 p.Ile192Val (c.574A>G) is classified Uncertain significance in CCDC69 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-25). AlphaMissense: likely benign (0.3087); Absent from gnomAD v4.1.

How common is CCDC69 p.Ile192Val (c.574A>G) in the general population?

CCDC69 p.Ile192Val (c.574A>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CCDC69 p.Ile192Val (c.574A>G)?

AlphaMissense predicts likely benign (score 0.3087) — an in-silico prediction, not a clinical call.

CCDC69 p.Ile192Val

c.574A>G · VCV3828740

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.3087 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.3087	likely benign
REVEL	0.113	moderately benign-leaning
SaProt	LLR -10.75	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.6	GERP 1.1, phastCons 1
Regional constraint	o/e 1.09	unconstrained · MANE · 41 kb · p 0.1 · regional, not allelic
Overall
CADD	21.6	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

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: CCDC69
Protein: p.Ile192Val
Coding: c.574A>G
MANE Select: NM_015621
Type: single nucleotide variant
Location: chr5:151185463 (GRCh38)
Gene constraint: LOEUF 1.181 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 85.55

Full CCDC69 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CCDC69 p.Ala110Thr Uncertain significance ★ ⚠ same type
CCDC69 p.Ala118Glu Uncertain significance ★ ⚠ same type
CCDC69 p.Ala118Thr Uncertain significance ★ ⚠ same type
CCDC69 p.Ala118Val Uncertain significance ★ ⚠ same type
CCDC69 p.Ala75Val Uncertain significance ★ ⚠ same type
CCDC69 p.Arg191Cys Uncertain significance ★ ⚠ same type
CCDC69 p.Arg191His Uncertain significance ★ ⚠ same type
CCDC69 p.Arg198Gln 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/ccdc69-p-ile192val (accessed [today's date]).

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