MAP1B p.His1999=
c.5997C>T · rs146865737 · VCV791091
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.226%, nfe)
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 -0.76 | GERP -2 |
| Overall | ||
| CADD | 3.069 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.226%
European (non-Finnish) · 2,662/1,180,018 alleles
Filtering AF
0.218%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.216%
Overall
0.193%
3,123/1,614,130 alleles · rare
exomes 2,875/1,461,864 · genomes 248/152,266 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.226% | 443 |
| South Asian | 0.186% | 539 |
| Admixed American | 0.133% | 750 |
| Remaining individualsnot grpmax-eligible | 0.131% | 762 |
| Finnishnot grpmax-eligible | 0.117% | 853 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0675% | 1,480 |
| Middle Eastern | 0.0495% | 2,021 |
| African / African-American | 0.0426% | 2,345 |
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.His1999=
- Coding
- c.5997C>T
- MANE Select
- NM_005909
- dbSNP
- rs146865737
- Type
- single nucleotide variant
- Location
- chr5:72199352 (GRCh38)
- Gene constraint
- LOEUF 0.105 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 46.18
- Residue 1999
- 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-his1999 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown