MAPT p.Pro442=
c.1326C>T · rs201312701 · VCV1209906
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.023%, nfe)
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 -5.3 | GERP -5.8 |
| Overall | ||
| CADD | 1.098 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.023%
European (non-Finnish) · 268/1,166,434 alleles
Filtering AF
0.0207%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0198%
Overall
0.0179%
283/1,579,434 alleles · ultra-rare
exomes 258/1,427,266 · genomes 25/152,168 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.023% | 4,352 |
| Finnishnot grpmax-eligible | 0.0112% | 8,900 |
| Remaining individualsnot grpmax-eligible | 0.00988% | 10,117 |
| African / African-American | 0.00274% | 36,441 |
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.Pro442=
- Coding
- c.1326C>T
- MANE Select
- NM_001377265
- dbSNP
- rs201312701
- Type
- single nucleotide variant
- Location
- chr17:45983905 (GRCh38)
- Gene constraint
- LOEUF 0.723 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 49.56 · 299 PDB
- Residue 442
- the 'disordered' region
Similar variants
- 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
- MAPT p.Gly727Ser 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-pro442 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown