MAGI2 p.Asp579=
c.1737C>T · rs142555732 · VCV286072
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0162%, nfe)
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 3.6 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 13.45 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0162%
European (non-Finnish) · 191/1,179,984 alleles
Filtering AF
0.0143%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0135%
Overall
0.0128%
207/1,614,046 alleles · ultra-rare
exomes 192/1,461,750 · genomes 15/152,296 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0162% | 6,178 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,814 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,606 |
| Finnishnot grpmax-eligible | 0.00312% | 32,011 |
| African / African-American | 0.00267% | 37,520 |
| South Asian | 0.0022% | 45,536 |
| Admixed American | 0.00167% | 60,020 |
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.Asp579=
- Coding
- c.1737C>T
- MANE Select
- NM_012301
- dbSNP
- rs142555732
- Type
- single nucleotide variant
- Location
- chr7:78256253 (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-asp579 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown