MAP1B p.Ser1731=
c.5193C>A · rs78388066 · VCV782815
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.84%, eas)
Conditions
2
hearing loss, autosomal dominant 83
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 0.57 | GERP 1.3, phastCons 1 |
| Overall | ||
| CADD | 7.376 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.84%
East Asian · 826/44,872 alleles
Filtering AF
1.74%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.7%
Overall
0.0684%
1,104/1,614,020 alleles · low-frequency
exomes 943/1,461,768 · genomes 161/152,252 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.84% | 54 |
| Remaining individualsnot grpmax-eligible | 0.309% | 324 |
| South Asian | 0.0593% | 1,687 |
| African / African-American | 0.0173% | 5,771 |
| Middle Eastern | 0.0165% | 6,062 |
| Admixed American | 0.0133% | 7,504 |
| European (non-Finnish) | 0.000763% | 131,112 |
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.Ser1731=
- Coding
- c.5193C>A
- MANE Select
- NM_005909
- dbSNP
- rs78388066
- Type
- single nucleotide variant
- Location
- chr5:72198548 (GRCh38)
- Gene constraint
- LOEUF 0.105 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 46.18
- Residue 1731
- 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 condition
- MAP1B p.Arg303Ter Pathogenic/Likely pathogenic ★★ same condition
- MAP1B p.Arg85Ter Pathogenic/Likely pathogenic ★★ same condition
- MAP1B p.Arg999Ter Pathogenic/Likely pathogenic ★★ same condition
- MAP1B p.Arg1399Cys Uncertain significance ★★ ⚠ same condition
- MAP1B p.Arg1948Trp Uncertain significance ★★ ⚠ same condition
- MAP1B p.Glu1944Lys Uncertain significance ★★ ⚠ same condition
- MAP1B p.Leu1453Val Uncertain significance ★★ ⚠ same condition
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-ser1731 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown