MAP2 p.Glu1129=
c.3387G>A · rs36091461 · VCV773129
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.91%, afr)
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 0.17 | GERP -4.8, phastCons 0.73 |
| Overall | ||
| CADD | 2.435 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.91%
African / African-American · 2,933/75,038 alleles
Filtering AF
3.79%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.74%
Overall
0.214%
3,458/1,614,096 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.91% | 26 |
| Admixed American | 0.315% | 318 |
| Remaining individualsnot grpmax-eligible | 0.314% | 319 |
| Middle Eastern | 0.28% | 357 |
| European (non-Finnish) | 0.00966% | 10,351 |
| South Asian | 0.00769% | 13,009 |
| East Asian | 0.00223% | 44,864 |
| Finnishnot grpmax-eligible | 0.00156% | 64,030 |
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.Glu1129=
- Coding
- c.3387G>A
- MANE Select
- NM_006838 · reported on NM_001375505
- dbSNP
- rs36091461
- Type
- single nucleotide variant
- Location
- chr2:209695557 (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.Glu179Gly 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-glu1129 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown