CACNA1F p.Glu804=
c.2412A>G · rs868954985 · VCV1156141
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0229%, amr)
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 -0.43 | GERP -2.4, phastCons 0.002 |
| Overall | ||
| CADD | 0.106 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0229%
Admixed American · 9/39,372 alleles
Filtering AF
0.0119%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00884%
Overall
0.00172%
19/1,106,386 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0229% | 4,375 |
| African / African-American | 0.00194% | 51,547 |
| European (non-Finnish) | 0.0011% | 91,075 |
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.Glu804=
- Coding
- c.2412A>G
- MANE Select
- NM_001256789
- dbSNP
- rs868954985
- Type
- single nucleotide variant
- Location
- chrX:49219765 (GRCh38)
- Structure
- AlphaFold pLDDT 67.46
- Residue 804
- the 'disordered' region
Similar variants
- 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
- CACNA1F c.3236+1G>A Pathogenic/Likely pathogenic ★★ same type
- CACNA1F c.381+1G>A 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/cacna1f-p-glu804 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown