MAP1B p.Ala1000=
c.3000C>T · rs148153706 · VCV780541
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
rare (popmax 0.478%, 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 -13 | GERP -4.8 |
| Overall | ||
| CADD | 0.045 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.478%
African / African-American · 358/74,896 alleles
Filtering AF
0.437%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.421%
Overall
0.0289%
466/1,613,796 alleles · rare
exomes 254/1,461,888 · genomes 212/151,908 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.478% | 209 |
| Remaining individualsnot grpmax-eligible | 0.0432% | 2,315 |
| Finnishnot grpmax-eligible | 0.0313% | 3,198 |
| Admixed American | 0.025% | 3,998 |
| South Asian | 0.00879% | 11,380 |
| European (non-Finnish) | 0.00314% | 31,891 |
| East Asian | 0.00223% | 44,860 |
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.Ala1000=
- Coding
- c.3000C>T
- MANE Select
- NM_005909
- dbSNP
- rs148153706
- Type
- single nucleotide variant
- Location
- chr5:72196355 (GRCh38)
- Gene constraint
- LOEUF 0.105 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 46.18
- Residue 1000
- the 'disordered' region; a UniProt-annotated variant site (in pvnh9)
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-ala1000 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown