MAP1A p.Ser2152=
c.6456A>G · rs201503662 · VCV747144
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.252%, 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 0.9 | GERP 0.52, phastCons 0.98 |
| Overall | ||
| CADD | 3.877 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.252%
African / African-American · 189/75,010 alleles
Filtering AF
0.223%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.211%
Overall
0.0128%
207/1,614,056 alleles · rare
exomes 89/1,461,862 · genomes 118/152,194 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.252% | 397 |
| Remaining individualsnot grpmax-eligible | 0.0208% | 4,808 |
| Admixed American | 0.00833% | 12,004 |
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
- MAP1A
- Protein
- p.Ser2152=
- Coding
- c.6456A>G
- MANE Select
- NM_002373
- dbSNP
- rs201503662
- Type
- single nucleotide variant
- Location
- chr15:43527929 (GRCh38)
- Structure
- AlphaFold pLDDT 94.44 · 41 PDB
Similar variants
- MAP1A p.Arg2734Gln Uncertain significance ★★ same type
- MAP1A p.Gly567Ala Uncertain significance ★★ ⚠ same type
- MAP1A p.Gly482= Benign/Likely benign ★★ same type
- MAP1A p.Leu1621Val Benign ★★ same type
- MAP1A p.Ser1152= Likely benign ★★ same type
- MAP1A p.Ser1311= Benign/Likely benign ★★ same type
- MAP1A p.Ser1544= Benign ★★ same type
- MAP1A p.Ser1858Cys 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/map1a-p-ser2152 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown