CACNA1F p.Ala207=
c.621G>A · rs1557111061 · VCV2065143
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000224%, 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 -7.1 | GERP -3.7 |
| Overall | ||
| CADD | 7.435 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000224%
European (non-Finnish) · 2/893,726 alleles
Filtering AF
3.7e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.4e-05%
Overall
0.000183%
2/1,094,443 alleles · very rare
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
- CACNA1F
- Protein
- p.Ala207=
- Coding
- c.621G>A
- MANE Select
- NM_001256789
- dbSNP
- rs1557111061
- Type
- single nucleotide variant
- Location
- chrX:49230510 (GRCh38)
- Structure
- AlphaFold pLDDT 67.46
Similar variants
- CACNA1F p.Ala207Val Uncertain significance ★ ⚠ same residue
- CACNA1F p.Ala207_Phe208insLeuArgAla Uncertain significance ★ same residue
- CACNA1F c.1118+1G>C Pathogenic ★★ same type
- CACNA1F c.2086-1G>C Pathogenic/Likely pathogenic ★★ same type
- CACNA1F c.2086-2A>G Pathogenic/Likely pathogenic ★★ same type
- CACNA1F c.2543+1G>A Pathogenic ★★ same type
- CACNA1F c.2674-2A>G Likely pathogenic ★★ same type
- CACNA1F c.2928+1G>A 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/cacna1f-p-ala207 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown