MAP2 p.Gln1760=
c.5280A>G · rs144328342 · VCV712992
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.449%, 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 0.48 | GERP -3.7, phastCons 0.78 |
| Overall | ||
| CADD | 1.034 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.449%
African / African-American · 337/75,032 alleles
Filtering AF
0.41%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.394%
Overall
0.151%
2,444/1,613,974 alleles · rare
exomes 2,130/1,461,718 · genomes 314/152,256 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.449% | 223 |
| Finnishnot grpmax-eligible | 0.173% | 577 |
| Remaining individualsnot grpmax-eligible | 0.149% | 672 |
| European (non-Finnish) | 0.147% | 682 |
| South Asian | 0.12% | 835 |
| Middle Eastern | 0.099% | 1,010 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0811% | 1,234 |
| Admixed American | 0.0583% | 1,714 |
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.Gln1760=
- Coding
- c.5280A>G
- MANE Select
- NM_001375505
- dbSNP
- rs144328342
- Type
- single nucleotide variant
- Location
- chr2:209730193 (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.Glu1129= 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-gln1760 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown