MAP2 p.His162=
c.486C>T · VCV4959556
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 26.2%, afr) — too common for a highly-penetrant pathogenic allele
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 -2 | GERP -5.1 |
| Overall | ||
| CADD | 7.006 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
26.2%
African / African-American · 19,144/73,180 alleles
Filtering AF
25.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 25.7%
Overall
8.35%
132,655/1,587,814 alleles · common
exomes 112,642/1,435,704 · genomes 20,013/152,110 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 26.2% | 4 |
| East Asian | 22.7% | 4 |
| South Asian | 14.6% | 7 |
| Middle Eastern | 12.7% | 8 |
| Ashkenazi Jewishnot grpmax-eligible | 10.5% | 10 |
| Remaining individualsnot grpmax-eligible | 9.57% | 10 |
| Finnishnot grpmax-eligible | 8.35% | 12 |
| Admixed American | 7.51% | 13 |
| European (non-Finnish) | 6.14% | 16 |
| Amishnot grpmax-eligible | 5.49% | 18 |
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.His162=
- Coding
- c.486C>T
- MANE Select
- NM_001375505
- Type
- single nucleotide variant
- Location
- chr2:209692656 (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-his162 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown