CTNND2 p.Arg504=
c.1512A>G · rs151074933 · VCV1277964
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.186%, afr)
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 0.057 | GERP -2.9, phastCons 0.97 |
| Overall | ||
| CADD | 9.454 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.186%
African / African-American · 139/74,626 alleles
Filtering AF
0.161%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.151%
Overall
0.0101%
162/1,605,266 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.186% | 537 |
| Middle Eastern | 0.0331% | 3,025 |
| Remaining individualsnot grpmax-eligible | 0.0225% | 4,443 |
| Admixed American | 0.0102% | 9,759 |
| South Asian | 0.00112% | 89,426 |
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
- CTNND2
- Protein
- p.Arg504=
- Coding
- c.1512A>G
- MANE Select
- NM_001332
- dbSNP
- rs151074933
- Type
- single nucleotide variant
- Location
- chr5:11346488 (GRCh38)
- Gene constraint
- LOEUF 0.228 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 58.88
Similar variants
- CTNND2 p.Arg504Ter Pathogenic ★ same residue
- CTNND2 p.Asp700Gly Uncertain significance ★★ ⚠ same type
- CTNND2 p.Asp802Asn Uncertain significance ★★ same type
- CTNND2 p.Glu217Asp Uncertain significance ★★ ⚠ same type
- CTNND2 c.1178-153T>C Likely benign ★★ same type
- CTNND2 c.1178-164G>A Benign ★★ same type
- CTNND2 c.1372+105T>C Likely benign ★★ same type
- CTNND2 c.1628+51C>T 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/ctnnd2-p-arg504 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown