CADM3 p.Val47=
c.141G>A · VCV4533692
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00653%, 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 0.13 | GERP -4.1, phastCons 0.77 |
| Overall | ||
| CADD | 7.084 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00653%
European (non-Finnish) · 77/1,179,962 alleles
Filtering AF
0.0053%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0049%
Overall
0.00496%
80/1,613,942 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00653% | 15,324 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,243 |
| African / African-American | 0.00134% | 74,906 |
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
- CADM3
- Protein
- p.Val47=
- Coding
- c.141G>A
- MANE Select
- NM_001127173
- Type
- single nucleotide variant
- Location
- chr1:159191988 (GRCh38)
- Gene constraint
- LOEUF 0.381 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 84.97 · 1 PDB
- Residue 47
- a β-strand; the ig-like v-type domain
Similar variants
- CADM3 p.Tyr138Cys Likely pathogenic ★★ same type
- CADM3 c.89-2102C>T Uncertain significance ★★ same type
- CADM3 p.Leu13Gln Uncertain significance ★★ ⚠ same type
- CADM3 p.Tyr354Cys Uncertain significance ★★ ⚠ same type
- CADM3 c.229+11A>G Uncertain significance ★ same type
- CADM3 c.382+1G>A Uncertain significance ★ same type
- CADM3 c.89-2118G>A Uncertain significance ★ same type
- CADM3 c.89-2133A>T 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/cadm3-p-val47 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown