MAGI2 p.Pro1038=
c.3114C>A · rs1282358138 · VCV762431
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000186%)
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 -2.8 | GERP -4.6 |
| Overall | ||
| CADD | 1.883 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000186%
Overall
0.000186%
3/1,612,678 alleles · very rare
exomes 2/1,460,602 · genomes 1/152,076 · joint denominator
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.Pro1038=
- Coding
- c.3114C>A
- MANE Select
- NM_012301
- dbSNP
- rs1282358138
- Type
- single nucleotide variant
- Location
- chr7:78132978 (GRCh38)
- Gene constraint
- LOEUF 0.369 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 61.10 · 5 PDB
- Residue 1038
- the 'disordered' region
Similar variants
- MAGI2 p.Pro1038Ala 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-pro1038 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown