MAP2 p.Gly1689=
c.5067G>T · rs541515893 · VCV733331
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.72%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.47 | donor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.18 | GERP -1.1, phastCons 0.063 |
| Overall | ||
| CADD | 15.02 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.72%
South Asian · 624/86,692 alleles
Filtering AF
0.673%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.654%
Overall
0.0412%
647/1,569,180 alleles · rare
exomes 615/1,416,928 · genomes 32/152,252 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.72% | 139 |
| Middle Eastern | 0.0333% | 3,001 |
| Remaining individualsnot grpmax-eligible | 0.0263% | 3,801 |
| African / African-American | 0.00678% | 14,749 |
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
- MAP2
- Protein
- p.Gly1689=
- Coding
- c.5067G>T
- MANE Select
- NM_001375505
- dbSNP
- rs541515893
- Type
- single nucleotide variant
- Location
- chr2:209710248 (GRCh38)
- Structure
- AlphaFold pLDDT 86.07 · 40 PDB
Similar variants
- MAP2 p.Ala1074Thr Uncertain significance ★★ ⚠ same type
- MAP2 p.Ala752Ser Uncertain significance ★★ ⚠ same type
- MAP2 p.Arg1715His Uncertain significance ★★ ⚠ same type
- MAP2 p.Val1359Ala Uncertain significance ★★ ⚠ same type
- MAP2 p.Ala414Ser Benign/Likely benign ★★ same type
- MAP2 p.Asp679= Benign ★★ same type
- MAP2 p.Gln1760= Benign/Likely benign ★★ same type
- MAP2 p.Glu1129= Benign ★★ 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/map2-p-gly1689 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown