GRIN2D p.Asp804=
c.2412C>T · rs147906766 · VCV1652894
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00467%, 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 1.7 | GERP 0.52, phastCons 1 |
| Overall | ||
| CADD | 11.57 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00467%
European (non-Finnish) · 55/1,178,870 alleles
Filtering AF
0.00367%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00329%
Overall
0.00354%
57/1,609,558 alleles · very rare
exomes 55/1,457,282 · genomes 2/152,276 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00467% | 21,434 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,352 |
| African / African-American | 0.00134% | 74,906 |
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
- GRIN2D
- Protein
- p.Asp804=
- Coding
- c.2412C>T
- MANE Select
- NM_000836
- dbSNP
- rs147906766
- Type
- single nucleotide variant
- Location
- chr19:48441928 (GRCh38)
- Gene constraint
- LOEUF 0.642 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 64.00 · 13 PDB
- Residue 804
- an α-helix
Similar variants
- GRIN2D p.Asp804Asn Uncertain significance ★ ⚠ same residue
- GRIN2D p.Met681Val Pathogenic/Likely pathogenic ★★ same type
- GRIN2D p.Val667Ile Pathogenic/Likely pathogenic ★★ same type
- GRIN2D p.Ala1032Val Uncertain significance ★★ ⚠ same type
- GRIN2D p.Ala1040Thr Uncertain significance ★★ ⚠ same type
- GRIN2D p.Ala1085Thr Uncertain significance ★★ ⚠ same type
- GRIN2D p.Ala1135Thr Uncertain significance ★★ ⚠ same type
- GRIN2D p.Ala1177Thr 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/grin2d-p-asp804 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown