GRID2 p.Glu56del
c.163GAG[1] · rs763741990 · VCV1929028
Uncertain significance
Multiple submitters
Classification
Uncertain significance
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0603%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.63 | GERP -2.1, phastCons 1 |
| Overall | ||
| CADD | 19.76 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0603%
East Asian · 27/44,810 alleles
Filtering AF
0.0425%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0365%
Overall
0.00211%
34/1,611,508 alleles · ultra-rare
exomes 33/1,459,358 · genomes 1/152,150 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0603% | 1,660 |
| European (non-Finnish) | 0.000594% | 168,256 |
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
- GRID2
- Protein
- p.Glu56del
- Coding
- c.163GAG[1]
- MANE Select
- NM_001510
- dbSNP
- rs763741990
- Type
- Microsatellite
- Location
- chr4:92590205 (GRCh38)
- Gene constraint
- LOEUF 0.332 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 76.07 · 6 PDB
- Residue 56
- the 'interaction with cbln1 homotrimer' region
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/grid2-p-glu56del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown