MAGI2 p.Pro585=
c.1755C>T · rs34937835 · VCV95509
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 8 submitters
gnomAD v4.1
Common
common (popmax 5.19%, 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 | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.092 | GERP -5.3, phastCons 0.054 |
| Overall | ||
| CADD | 11.0 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
5.19%
East Asian · 2,326/44,806 alleles
Filtering AF
5.02%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.94%
Overall
1.72%
27,739/1,614,008 alleles · common
exomes 25,342/1,461,722 · genomes 2,397/152,286 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 5.19% | 19 |
| Finnishnot grpmax-eligible | 4.71% | 21 |
| Admixed American | 4.69% | 21 |
| European (non-Finnish) | 1.53% | 65 |
| Remaining individualsnot grpmax-eligible | 1.39% | 72 |
| South Asian | 0.367% | 273 |
| Ashkenazi Jewishnot grpmax-eligible | 0.304% | 329 |
| African / African-American | 0.275% | 364 |
| Middle Eastern | 0.149% | 673 |
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.Pro585=
- Coding
- c.1755C>T
- MANE Select
- NM_012301
- dbSNP
- rs34937835
- Type
- single nucleotide variant
- Location
- chr7:78256235 (GRCh38)
- Gene constraint
- LOEUF 0.369 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 61.10 · 5 PDB
Similar variants
- 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
- MAGI2 p.Ala899Pro 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-pro585 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown