MAP2 p.Glu39=
c.117A>G · rs148825736 · VCV774839
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0192%, 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 0.38 | GERP -1.9, phastCons 0.76 |
| Overall | ||
| CADD | 6.287 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0192%
European (non-Finnish) · 227/1,180,024 alleles
Filtering AF
0.0171%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0163%
Overall
0.0146%
236/1,614,034 alleles · ultra-rare
exomes 216/1,461,830 · genomes 20/152,204 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0192% | 5,198 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,414 |
| African / African-American | 0.004% | 24,975 |
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.Glu39=
- Coding
- c.117A>G
- MANE Select
- NM_001375505
- dbSNP
- rs148825736
- Type
- single nucleotide variant
- Location
- chr2:209653287 (GRCh38)
- Structure
- AlphaFold pLDDT 86.07 · 40 PDB
- Residue 39
- the 'disordered' region
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-glu39 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown