MAP1B p.Pro593=
c.1779A>G · rs61375284 · VCV789740
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.8%, 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 -2.6 | GERP -4.8 |
| Overall | ||
| CADD | 0.462 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.8%
African / African-American · 1,352/75,000 alleles
Filtering AF
1.72%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.69%
Overall
0.0931%
1,502/1,613,740 alleles · low-frequency
exomes 726/1,461,500 · genomes 776/152,240 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.8% | 55 |
| Admixed American | 0.112% | 896 |
| Remaining individualsnot grpmax-eligible | 0.11% | 906 |
| Middle Eastern | 0.033% | 3,031 |
| South Asian | 0.00549% | 18,212 |
| European (non-Finnish) | 0.000593% | 168,537 |
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.Pro593=
- Coding
- c.1779A>G
- MANE Select
- NM_005909
- dbSNP
- rs61375284
- Type
- single nucleotide variant
- Location
- chr5:72195134 (GRCh38)
- Gene constraint
- LOEUF 0.105 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 46.18
- Residue 593
- the 'disordered' region; a UniProt-annotated variant site (in pvnh9)
Similar variants
- MAP1B p.Pro593Ala Uncertain significance ★ ⚠ same residue
- 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
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-pro593 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown