Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 10 submitters
gnomAD v4.1
Common
common (popmax 91%, afr) — too common for a highly-penetrant pathogenic allele
Conditions
1
nephrotic syndrome 15
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 -0.88 | GERP -4.5, phastCons 0.012 |
| Overall | ||
| CADD | 5.619 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
91%
African / African-American · 68,256/74,970 alleles
Filtering AF
90.5%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 90.2%
Overall
85.7%
1,371,893/1,601,268 alleles · common
exomes 1,241,572/1,449,150 · genomes 130,321/152,118 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 91% | 1 |
| European (non-Finnish) | 87.8% | 1 |
| Finnishnot grpmax-eligible | 87.7% | 1 |
| Remaining individualsnot grpmax-eligible | 84.4% | 1 |
| Ashkenazi Jewishnot grpmax-eligible | 80.2% | 1 |
| Middle Eastern | 80.1% | 1 |
| South Asian | 76.9% | 1 |
| Admixed American | 72.3% | 1 |
| Amishnot grpmax-eligible | 69.3% | 1 |
| East Asian | 59.3% | 2 |
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.Ser1071=
- Coding
- c.3213G>A
- MANE Select
- NM_012301
- dbSNP
- rs7812015
- Type
- single nucleotide variant
- Location
- chr7:78127407 (GRCh38)
- Gene constraint
- LOEUF 0.369 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 61.10 · 5 PDB
- Residue 1071
- the 'disordered' region
Similar variants
- MAGI2 p.Ala1028Val Uncertain significance ★★ ⚠ same condition
- MAGI2 p.Ala1247Thr Uncertain significance ★★ ⚠ same condition
- MAGI2 p.Ala1271Thr Uncertain significance ★★ ⚠ same condition
- MAGI2 p.Ala1453Thr Uncertain significance ★★ ⚠ same condition
- MAGI2 p.Ala620Gly Uncertain significance ★★ ⚠ same condition
- MAGI2 p.Ala899Pro Uncertain significance ★★ ⚠ same condition
- MAGI2 p.Arg1370Pro Uncertain significance ★★ ⚠ same condition
- MAGI2 p.Arg408Gln Uncertain significance ★★ ⚠ same condition
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-ser1071 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown