MAGI2 p.Val455=
c.1365G>C · rs750615832 · VCV2902715
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0626%, amr)
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 -0.06 | GERP -0.065, phastCons 0.61 |
| Overall | ||
| CADD | 7.01 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0626%
Admixed American · 37/59,074 alleles
Filtering AF
0.0466%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0411%
Overall
0.0023%
37/1,610,116 alleles · ultra-rare
exomes 34/1,457,992 · genomes 3/152,124 · 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.Val455=
- Coding
- c.1365G>C
- MANE Select
- NM_012301
- dbSNP
- rs750615832
- Type
- single nucleotide variant
- Location
- chr7:78343821 (GRCh38)
- Gene constraint
- LOEUF 0.369 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 61.10 · 5 PDB
- Residue 455
- a β-strand; the pdz 2 domain
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-val455 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown