CADM1 p.Val409=
c.1227C>G · rs757194461 · VCV745104
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00833%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.246 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.28 | GERP -1.3, phastCons 0.94 |
| Overall | ||
| CADD | 5.762 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00833%
Admixed American · 5/59,990 alleles
Filtering AF
0.00323%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00207%
Overall
0.000434%
7/1,613,688 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00833% | 11,998 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,242 |
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
- CADM1
- Protein
- p.Val409=
- Coding
- c.1227C>G
- MANE Select
- NM_001301043
- dbSNP
- rs757194461
- Type
- single nucleotide variant
- Location
- chr11:115178714 (GRCh38)
- Gene constraint
- LOEUF 0.422 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 81.63 · 2 PDB
Similar variants
- CADM1 p.Val409Ile Uncertain significance ★ ⚠ same residue
- CADM1 p.Ala226= Benign ★★ same type
- CADM1 p.Ala262= Benign ★★ same type
- CADM1 p.Asn301= Benign ★★ same type
- CADM1 p.Asp307= Benign ★★ same type
- CADM1 p.Thr336Ile Likely benign ★★ same type
- CADM1 p.Ala156Val Uncertain significance ★ ⚠ same type
- CADM1 p.Ala262Thr 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/cadm1-p-val409 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown