CADM1 p.Val4=
c.12A>G · rs45514793 · VCV710449
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.743%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.14 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 2.4 | GERP 1.3, phastCons 1 |
| Overall | ||
| CADD | 10.71 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.743%
African / African-American · 543/73,076 alleles
Filtering AF
0.691%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.671%
Overall
0.0605%
936/1,546,892 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.743% | 135 |
| Ashkenazi Jewishnot grpmax-eligible | 0.175% | 572 |
| Admixed American | 0.145% | 688 |
| Remaining individualsnot grpmax-eligible | 0.0968% | 1,033 |
| Middle Eastern | 0.0191% | 5,242 |
| European (non-Finnish) | 0.018% | 5,564 |
| South Asian | 0.00476% | 20,990 |
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.Val4=
- Coding
- c.12A>G
- MANE Select
- NM_001301043
- dbSNP
- rs45514793
- Type
- single nucleotide variant
- Location
- chr11:115504383 (GRCh38)
- Gene constraint
- LOEUF 0.422 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 81.63 · 2 PDB
Similar variants
- CADM1 p.Val4Glu 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-val4 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown