Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 7 submitters
gnomAD v4.1
Common
common (popmax 58.6%, eas) — too common for a highly-penetrant pathogenic allele
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 -2.8 | GERP -2.6 |
| Overall | ||
| CADD | 5.899 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
58.6%
East Asian · 13,823/23,576 alleles
Filtering AF
57.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 57.5%
Overall
21.5%
242,861/1,128,038 alleles · common
exomes 201,647/982,416 · genomes 41,214/145,622 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 58.6% | 2 |
| African / African-American | 40.9% | 2 |
| South Asian | 34.1% | 3 |
| Admixed American | 32.6% | 3 |
| Ashkenazi Jewishnot grpmax-eligible | 27.6% | 4 |
| Remaining individualsnot grpmax-eligible | 25.1% | 4 |
| Middle Eastern | 25% | 4 |
| Finnishnot grpmax-eligible | 23.2% | 4 |
| Amishnot grpmax-eligible | 21% | 5 |
| European (non-Finnish) | 18.5% | 5 |
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
- MAGI2
- Protein
- p.Pro1423=
- Coding
- c.4269G>C
- MANE Select
- NM_012301
- dbSNP
- rs2960452
- Type
- single nucleotide variant
- Location
- chr7:78019414 (GRCh38)
- Gene constraint
- LOEUF 0.369 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 61.10 · 5 PDB
- Residue 1423
- the 'disordered' region
Similar variants
- MAGI2 p.Pro1423Ser Uncertain significance ★ ⚠ same residue
- MAGI2 p.Ala1028Val Uncertain significance ★★ ⚠ same type
- MAGI2 p.Ala1247Thr Uncertain significance ★★ ⚠ same type
- MAGI2 p.Ala1271Thr Uncertain significance ★★ ⚠ same type
- MAGI2 p.Ala1453Thr Uncertain significance ★★ ⚠ same type
- MAGI2 p.Ala274Thr Uncertain significance ★★ ⚠ same type
- MAGI2 p.Ala620Gly Uncertain significance ★★ ⚠ same type
- MAGI2 p.Ala809Ser Uncertain significance ★★ ⚠ 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/magi2-p-pro1423 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown