Is CCDC42 p.Arg16Pro (c.47G>C) pathogenic?

CCDC42 p.Arg16Pro (c.47G>C) is classified Uncertain significance in CCDC42 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-07). AlphaMissense: ambiguous (0.409); Absent from gnomAD v4.1.

How common is CCDC42 p.Arg16Pro (c.47G>C) in the general population?

CCDC42 p.Arg16Pro (c.47G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CCDC42 p.Arg16Pro (c.47G>C)?

AlphaMissense predicts ambiguous (score 0.409) — an in-silico prediction, not a clinical call.

CCDC42 p.Arg16Pro

c.47G>C · VCV3997027

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.409 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.409	ambiguous
REVEL	0.228	benign-leaning
SaProt	LLR -6.10	tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.6	GERP 0.82, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 14 kb · p 0.066 · regional, not allelic
Overall
CADD	24.1	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: CCDC42
Protein: p.Arg16Pro
Coding: c.47G>C
MANE Select: NM_144681
Type: single nucleotide variant
Location: chr17:8744563 (GRCh38)
Gene constraint: LOEUF 1.222 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.54

Full CCDC42 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CCDC42 p.Ala107Thr Uncertain significance ★ ⚠ same type
CCDC42 p.Ala111Asp Uncertain significance ★ ⚠ same type
CCDC42 p.Ala134Thr Uncertain significance ★ ⚠ same type
CCDC42 p.Ala199Ser Uncertain significance ★ ⚠ same type
CCDC42 p.Ala262Thr Uncertain significance ★ ⚠ same type
CCDC42 p.Arg104Gln Uncertain significance ★ ⚠ same type
CCDC42 p.Arg136Gln Uncertain significance ★ ⚠ same type
CCDC42 p.Arg198His 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/ccdc42-p-arg16pro (accessed [today's date]).

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