MAPRE2 p.Ser52=
c.156G>A · rs139112293 · VCV3042970
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00894%, sas)
Conditions
1
MAPRE2-related disorder
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 4.4 | GERP -5.8, phastCons 1 |
| Overall | ||
| CADD | 14.21 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00894%
South Asian · 8/89,502 alleles
Filtering AF
0.00443%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00317%
Overall
0.00267%
43/1,607,494 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00894% | 11,188 |
| African / African-American | 0.00537% | 18,612 |
| Finnishnot grpmax-eligible | 0.0047% | 21,297 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,120 |
| European (non-Finnish) | 0.00212% | 47,099 |
| Admixed American | 0.0017% | 58,902 |
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.Ser52=
- Coding
- c.156G>A
- MANE Select
- NM_014268
- dbSNP
- rs139112293
- Type
- single nucleotide variant
- Location
- chr18:35070228 (GRCh38)
- Gene constraint
- LOEUF 0.494 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 75.12
Disease context
MAPRE2-related disorder
Similar variants
- MAPRE2 c.86+1G>A Uncertain significance ★ same condition
- 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
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-ser52 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown