AP2M1 p.Phe79=
c.237C>T · rs11539598 · VCV1618766
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0766%, 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 -1.1 | GERP -3, phastCons 0.001 |
| Overall | ||
| CADD | 12.52 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0766%
European (non-Finnish) · 904/1,180,042 alleles
Filtering AF
0.0724%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0707%
Overall
0.0593%
958/1,614,160 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0766% | 1,305 |
| Remaining individualsnot grpmax-eligible | 0.0352% | 2,841 |
| Finnishnot grpmax-eligible | 0.0219% | 4,572 |
| Admixed American | 0.015% | 6,668 |
| East Asian | 0.00446% | 22,443 |
| South Asian | 0.00439% | 22,770 |
| African / African-American | 0.004% | 25,013 |
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
- AP2M1
- Protein
- p.Phe79=
- Coding
- c.237C>T
- MANE Select
- NM_004068
- dbSNP
- rs11539598
- Type
- single nucleotide variant
- Location
- chr3:184179019 (GRCh38)
- Gene constraint
- LOEUF 0.182 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 89.44 · 3 PDB
- Residue 79
- an α-helix
Similar variants
- AP2M1 p.Arg170Trp Pathogenic/Likely pathogenic ★★ same type
- AP2M1 p.Ala28Thr Uncertain significance ★★ ⚠ same type
- AP2M1 p.Arg169His Uncertain significance ★★ ⚠ same type
- AP2M1 p.Arg199Gln Uncertain significance ★★ ⚠ same type
- AP2M1 p.Arg40Trp Uncertain significance ★★ ⚠ same type
- AP2M1 p.Arg44His Uncertain significance ★★ ⚠ same type
- AP2M1 p.Cys246Arg Uncertain significance ★★ ⚠ same type
- AP2M1 p.Cys86Tyr Uncertain significance ★★ ⚠ 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/ap2m1-p-phe79 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown