CACNA1F p.Glu802=
c.2406G>A · rs185037790 · VCV2660520
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00982%, sas)
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 -0.51 | GERP -2.2, phastCons 0.076 |
| Overall | ||
| CADD | 0.278 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00982%
South Asian · 5/50,937 alleles
Filtering AF
0.00383%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00248%
Overall
0.000917%
10/1,090,161 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00982% | 10,187 |
| Admixed American | 0.00767% | 13,038 |
| Finnishnot grpmax-eligible | 0.00232% | 43,033 |
| Remaining individualsnot grpmax-eligible | 0.00229% | 43,606 |
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.Glu802=
- Coding
- c.2406G>A
- MANE Select
- NM_001256789
- dbSNP
- rs185037790
- Type
- single nucleotide variant
- Location
- chrX:49219771 (GRCh38)
- Structure
- AlphaFold pLDDT 67.46
- Residue 802
- 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-glu802 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown