MAPRE2 p.Asn129=
c.387C>T · rs750392221 · VCV782613
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0167%, amr)
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 0.099 | GERP -3.6, phastCons 0.98 |
| Overall | ||
| CADD | 9.329 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0167%
Admixed American · 10/59,804 alleles
Filtering AF
0.00903%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00683%
Overall
0.00136%
22/1,611,936 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0167% | 5,980 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,364 |
| South Asian | 0.0011% | 90,866 |
| European (non-Finnish) | 0.000848% | 117,918 |
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
- MAPRE2
- Protein
- p.Asn129=
- Coding
- c.387C>T
- MANE Select
- NM_014268
- dbSNP
- rs750392221
- Type
- single nucleotide variant
- Location
- chr18:35097582 (GRCh38)
- Gene constraint
- LOEUF 0.494 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 75.12
- Residue 129
- the calponin-homology (ch) domain
Similar variants
- MAPRE2 p.Arg143Cys Pathogenic/Likely pathogenic ★★ same type
- MAPRE2 p.Glu318Lys Uncertain significance ★★ ⚠ same type
- MAPRE2 p.Ser28Ter Uncertain significance ★★ same type
- MAPRE2 c.250+8A>T Benign/Likely benign ★★ same type
- MAPRE2 p.Gly260= Benign ★★ same type
- MAPRE2 p.His282= Benign/Likely benign ★★ same type
- MAPRE2 p.Pro322= Benign ★★ same type
- MAPRE2 p.Arg173Gln Likely pathogenic ★ 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/mapre2-p-asn129 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown