MAP2 p.Gln1036=
c.3108A>G · rs781042374 · VCV741646
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0467%, amr)
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 -0.18 | GERP -1.2 |
| Overall | ||
| CADD | 3.741 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0467%
Admixed American · 28/59,966 alleles
Filtering AF
0.0332%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0286%
Overall
0.0018%
29/1,613,838 alleles · ultra-rare
exomes 28/1,461,670 · genomes 1/152,168 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0467% | 2,142 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,482 |
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.Gln1036=
- Coding
- c.3108A>G
- MANE Select
- NM_001375505
- dbSNP
- rs781042374
- Type
- single nucleotide variant
- Location
- chr2:209695278 (GRCh38)
- Structure
- AlphaFold pLDDT 86.07 · 40 PDB
Similar variants
- MAP2 p.Gln1036Glu Uncertain significance ★ ⚠ same residue
- 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
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-gln1036 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown