CAMTA1 p.Ser853=
c.2559G>A · rs370492903 · VCV1694486
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0176%, mid)
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 -5.4 | GERP -3.4 |
| Overall | ||
| CADD | 0.44 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0176%
Middle Eastern · 1/5,678 alleles
Filtering AF
0.00644%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00598%
Overall
0.00653%
100/1,531,216 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0176% | 5,678 |
| European (non-Finnish) | 0.00779% | 12,830 |
| African / African-American | 0.0069% | 14,502 |
| East Asian | 0.00452% | 22,102 |
| Admixed American | 0.00413% | 24,185 |
| Remaining individualsnot grpmax-eligible | 0.00169% | 59,006 |
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.Ser853=
- Coding
- c.2559G>A
- MANE Select
- NM_015215
- dbSNP
- rs370492903
- Type
- single nucleotide variant
- Location
- chr1:7665106 (GRCh38)
- Gene constraint
- LOEUF 0.227 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 51.94 · 1 PDB
Similar variants
- 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
- CAMTA1 p.Arg1641Ter Pathogenic/Likely pathogenic ★★ same type
- CAMTA1 p.Arg982Ter 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-ser853 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown