MAP1B p.Asp2403=
c.7209C>T · VCV4821419
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.015%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.3 | GERP -5.1 |
| Overall | ||
| CADD | 7.957 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.015%
Admixed American · 9/60,002 alleles
Filtering AF
0.00773%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00579%
Overall
0.00676%
109/1,613,010 alleles · ultra-rare
exomes 105/1,460,872 · genomes 4/152,138 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.015% | 6,667 |
| African / African-American | 0.00935% | 10,695 |
| European (non-Finnish) | 0.0072% | 13,883 |
| East Asian | 0.00446% | 22,441 |
| South Asian | 0.00439% | 22,759 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,198 |
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
- MAP1B
- Protein
- p.Asp2403=
- Coding
- c.7209C>T
- MANE Select
- NM_005909
- Type
- single nucleotide variant
- Location
- chr5:72203759 (GRCh38)
- Gene constraint
- LOEUF 0.105 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 46.18
- Residue 2403
- a UniProt-annotated variant site (in pvnh9); a UniProt-annotated variant site (in pvnh9; no effect on protein expression); the 'mediates interaction with tmem185a' 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-asp2403 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown