MAPT p.Ala259=
c.777C>T · rs370558032 · VCV772739
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0774%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.49 | GERP 2.3 |
| Overall | ||
| CADD | 3.871 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0774%
African / African-American · 58/74,926 alleles
Filtering AF
0.0614%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0557%
Overall
0.00442%
71/1,607,844 alleles · ultra-rare
exomes 34/1,455,514 · genomes 37/152,330 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0774% | 1,292 |
| Remaining individualsnot grpmax-eligible | 0.0113% | 8,886 |
| East Asian | 0.0112% | 8,931 |
| Admixed American | 0.00168% | 59,468 |
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
- MAPT
- Protein
- p.Ala259=
- Coding
- c.777C>T
- MANE Select
- NM_001377265
- dbSNP
- rs370558032
- Type
- single nucleotide variant
- Location
- chr17:45983356 (GRCh38)
- Gene constraint
- LOEUF 0.723 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 49.56 · 299 PDB
- Residue 259
- the 'disordered' region
Similar variants
- MAPT p.Ala259Thr Uncertain significance ★ ⚠ same residue
- MAPT c.1999-10G>T Pathogenic ★★ same type
- MAPT c.2091+16C>T Pathogenic ★★ same type
- MAPT c.2091+3G>A Pathogenic ★★ same type
- MAPT p.Arg798Trp Pathogenic ★★ ⚠ same type
- MAPT p.Asn671Lys Pathogenic ★★ ⚠ same type
- MAPT p.Asn688= Pathogenic ★★ same type
- MAPT p.Gln728His Pathogenic/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/mapt-p-ala259 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown