APAF1 p.Ser807=
c.2421T>G · rs143097832 · VCV3034869
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.669%, afr)
Conditions
1
APAF1-related disorder
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 0.3 | GERP -2, phastCons 1 |
| Overall | ||
| CADD | 6.392 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.669%
African / African-American · 502/75,074 alleles
Filtering AF
0.62%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.601%
Overall
0.0343%
553/1,614,222 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.669% | 150 |
| Middle Eastern | 0.066% | 1,516 |
| Remaining individualsnot grpmax-eligible | 0.0432% | 2,315 |
| Admixed American | 0.025% | 4,002 |
| European (non-Finnish) | 0.000424% | 236,007 |
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
- APAF1
- Protein
- p.Ser807=
- Coding
- c.2421T>G
- MANE Select
- NM_181861
- dbSNP
- rs143097832
- Type
- single nucleotide variant
- Location
- chr12:98699524 (GRCh38)
- Gene constraint
- LOEUF 0.664 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.60 · 14 PDB
Disease context
APAF1-related disorder
Similar variants
- APAF1 c.3457-7T>C Likely benign same condition
- APAF1 c.527-10C>T Likely benign same condition
- APAF1 c.956-4A>T Likely benign same condition
- APAF1 c.*3T>C Benign same condition
- APAF1 p.Ala304= Likely benign same condition
- APAF1 p.Ala984= Benign same condition
- APAF1 p.Gln416= Likely benign same condition
- APAF1 p.Ile1038Val Benign same condition
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/apaf1-p-ser807 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown