MAP1B p.Ala2288Ser
c.6862G>T · VCV4721521
Computational evidence
| Protein change | ||
| AlphaMissense | 0.0957 | likely benign |
|---|---|---|
| REVEL | 0.021 | moderately benign-leaning |
| SaProt | LLR -5.72 | tolerated |
| ⇒ AlphaMissense, REVEL and SaProt all call this tolerated. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 7.5 | GERP 2.2, phastCons 1 |
| Regional constraint | o/e 0.71 | unconstrained · MANE · 5,431 bp · p 1.1e-08 · regional, not allelic |
| Overall | ||
| CADD | 21.0 | PHRED · no single calibrated threshold — expert panels disagree |
ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- MAP1B
- Protein
- p.Ala2288Ser
- Coding
- c.6862G>T
- MANE Select
- NM_005909
- Type
- single nucleotide variant
- Location
- chr5:72200217 (GRCh38)
- Gene constraint
- LOEUF 0.105 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 46.18
- Residue 2288
- a UniProt-annotated variant site (in pvnh9); a UniProt-annotated variant site (in pvnh9; no effect on protein expression); the 'disordered' region
Similar variants
- MAP1B p.Arg1664Ter Pathogenic/Likely pathogenic ★★ same type
- MAP1B p.Arg2140Ter Pathogenic ★★ same type
- MAP1B p.Arg303Ter Pathogenic/Likely pathogenic ★★ same type
- MAP1B p.Arg85Ter Pathogenic/Likely pathogenic ★★ same type
- MAP1B p.Arg999Ter Pathogenic/Likely pathogenic ★★ same type
- MAP1B p.Ala966Val Uncertain significance ★★ ⚠ same type
- MAP1B p.Arg1399Cys Uncertain significance ★★ ⚠ same type
- MAP1B p.Arg1948Trp Uncertain significance ★★ ⚠ 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/map1b-p-ala2288ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown