Is CCNA2 p.Arg47= (c.141G>A) pathogenic?

CCNA2 p.Arg47= (c.141G>A) is classified Likely benign in CCNA2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-11-18). Very rare (popmax 0.00161%, nfe).

How common is CCNA2 p.Arg47= (c.141G>A) in the general population?

CCNA2 p.Arg47= (c.141G>A) is very rare (popmax 0.00161%, nfe) (gnomAD).

CCNA2 p.Arg47=

c.141G>A · VCV4968367

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00161%, 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 0.07	GERP -1.3, phastCons 0.94
Overall
CADD	13.16	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00161% European (non-Finnish) · 19/1,179,830 alleles

Filtering AF 0.00103% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00083%

Overall 0.0013% 19/1,461,078 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: CCNA2
Protein: p.Arg47=
Coding: c.141G>A
MANE Select: NM_001237
Type: single nucleotide variant
Location: chr4:121823488 (GRCh38)
Gene constraint: LOEUF 0.183 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 73.80 · 115 PDB

Full CCNA2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CCN1 p.Arg47Pro Uncertain significance ★ ⚠ same residue
EXOSC9 p.Ala438Val Uncertain significance ★★ ⚠ same type
CCN1 c.277+50G>C Benign ★★ same type
CCN1 c.64-124G>A Benign ★★ same type
CCN1 c.-107C>A Benign ★★ same type
CCN1 p.Ser316Cys Likely benign ★★ ⚠ same type
CCN1 p.Tyr300= Benign ★★ same type
CCNA2 c.*828C>G 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/ccna2-p-arg47 (accessed [today's date]).

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