CAMTA1 p.Ala552=
c.1656G>A · rs112486808 · VCV2416206
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0853%, 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 -5.6 | GERP -4.4 |
| Overall | ||
| CADD | 0.442 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0853%
African / African-American · 64/75,040 alleles
Filtering AF
0.0685%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0624%
Overall
0.00701%
113/1,612,644 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0853% | 1,173 |
| Remaining individualsnot grpmax-eligible | 0.0448% | 2,232 |
| East Asian | 0.0201% | 4,986 |
| Middle Eastern | 0.0165% | 6,062 |
| Admixed American | 0.00333% | 30,016 |
| South Asian | 0.00329% | 30,362 |
| European (non-Finnish) | 0.000508% | 196,670 |
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
- CAMTA1
- Protein
- p.Ala552=
- Coding
- c.1656G>A
- MANE Select
- NM_015215
- dbSNP
- rs112486808
- Type
- single nucleotide variant
- Location
- chr1:7664203 (GRCh38)
- Gene constraint
- LOEUF 0.227 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 51.94 · 1 PDB
Similar variants
- CAMTA1 p.Ala552Val Uncertain significance ★ ⚠ same residue
- CAMTA1 p.Ala552Thr Likely benign ★ same residue
- CAMTA1 c.3342+1G>T Likely pathogenic ★★ same type
- CAMTA1 c.4183-1G>A Likely pathogenic ★★ same type
- CAMTA1 p.Arg1048Ter Pathogenic ★★ same type
- CAMTA1 p.Arg1411Ter Pathogenic/Likely pathogenic ★★ same type
- CAMTA1 p.Arg1582Ter Pathogenic/Likely pathogenic ★★ same type
- CAMTA1 p.Arg1594Ter Pathogenic/Likely pathogenic ★★ 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/camta1-p-ala552 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown