MAP1A p.Pro783=
c.2349A>T · rs373784417 · VCV747142
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.072%, 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 0.44 | GERP -0.31, phastCons 0.94 |
| Overall | ||
| CADD | 6.294 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.072%
African / African-American · 54/75,048 alleles
Filtering AF
0.0566%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0511%
Overall
0.00366%
59/1,614,062 alleles · ultra-rare
exomes 25/1,461,768 · genomes 34/152,294 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.072% | 1,390 |
| Admixed American | 0.00666% | 15,006 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,508 |
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
- MAP1A
- Protein
- p.Pro783=
- Coding
- c.2349A>T
- MANE Select
- NM_002373
- dbSNP
- rs373784417
- Type
- single nucleotide variant
- Location
- chr15:43523822 (GRCh38)
- Structure
- AlphaFold pLDDT 94.44 · 41 PDB
Similar variants
- MAP1A p.Arg2734Gln Uncertain significance ★★ same type
- MAP1A p.Gly567Ala Uncertain significance ★★ ⚠ same type
- MAP1A p.Gly482= Benign/Likely benign ★★ same type
- MAP1A p.Leu1621Val Benign ★★ same type
- MAP1A p.Ser1152= Likely benign ★★ same type
- MAP1A p.Ser1311= Benign/Likely benign ★★ same type
- MAP1A p.Ser1544= Benign ★★ same type
- MAP1A p.Ser1858Cys Likely benign ★★ 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/map1a-p-pro783 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown