MAPRE2 p.Gln89=
c.267A>G · rs543332831 · VCV2715958
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.011%, sas)
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 3.6 | GERP -1.7, phastCons 1 |
| Overall | ||
| CADD | 10.42 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.011%
South Asian · 10/91,068 alleles
Filtering AF
0.00716%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00668%
Overall
0.00731%
118/1,613,836 alleles · ultra-rare
exomes 109/1,461,530 · genomes 9/152,306 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.011% | 9,107 |
| European (non-Finnish) | 0.00856% | 11,681 |
| Admixed American | 0.005% | 20,005 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,829 |
| Finnishnot grpmax-eligible | 0.00156% | 64,012 |
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.Gln89=
- Coding
- c.267A>G
- MANE Select
- NM_014268
- dbSNP
- rs543332831
- Type
- single nucleotide variant
- Location
- chr18:35097462 (GRCh38)
- Gene constraint
- LOEUF 0.494 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 75.12
- Residue 89
- 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-gln89 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown