GRIN2D p.Arg963=
c.2889C>A · rs976061661 · VCV2091841
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00683%, afr)
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 1 | GERP -0.16, phastCons 1 |
| Overall | ||
| CADD | 8.296 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00683%
African / African-American · 4/58,528 alleles
Filtering AF
0.00229%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00137%
Overall
0.000371%
4/1,077,286 alleles · very rare
exomes 0/930,078 · genomes 4/147,208 · 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
- GRIN2D
- Protein
- p.Arg963=
- Coding
- c.2889C>A
- MANE Select
- NM_000836
- dbSNP
- rs976061661
- Type
- single nucleotide variant
- Location
- chr19:48442815 (GRCh38)
- Gene constraint
- LOEUF 0.642 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 64.00 · 13 PDB
Similar variants
- GRIN2D p.Arg963His Uncertain significance ★★ ⚠ same residue
- GRIN2D p.Arg963Cys Uncertain significance ★ ⚠ same residue
- GRIN2D p.Arg963fs 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
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-arg963 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown