GRIN2D p.Ser138=
c.414G>A · rs545376716 · VCV1609411
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.996%, afr)
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 0.82 | GERP -2.9, phastCons 1 |
| Overall | ||
| CADD | 12.6 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.996%
African / African-American · 676/67,886 alleles
Filtering AF
0.934%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.909%
Overall
0.065%
944/1,451,792 alleles · rare
exomes 434/1,299,666 · genomes 510/152,126 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.996% | 100 |
| Middle Eastern | 0.265% | 378 |
| Admixed American | 0.24% | 416 |
| Remaining individualsnot grpmax-eligible | 0.14% | 715 |
| European (non-Finnish) | 0.0075% | 13,334 |
| South Asian | 0.00265% | 37,704 |
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.Ser138=
- Coding
- c.414G>A
- MANE Select
- NM_000836
- dbSNP
- rs545376716
- Type
- single nucleotide variant
- Location
- chr19:48398806 (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.Ser138Ala Conflicting classifications of pathogenicity ★ ⚠ same residue
- GRIN2D p.Ser138Leu 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
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-ser138 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown