GRIN1 p.Ser129=
c.387G>C · rs199799811 · VCV391064
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
Conditions
1
neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal dominant
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 -6.1 | GERP -2.4 |
| Overall | ||
| CADD | 0.27 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,062 alleles
Filtering AF
0.00323%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00206%
Overall
0.00254%
41/1,614,028 alleles · ultra-rare
exomes 34/1,461,690 · genomes 7/152,338 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,062 |
| Admixed American | 0.00833% | 12,006 |
| African / African-American | 0.00666% | 15,013 |
| European (non-Finnish) | 0.00246% | 40,690 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,510 |
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
- GRIN1
- Protein
- p.Ser129=
- Coding
- c.387G>C
- MANE Select
- NM_007327
- dbSNP
- rs199799811
- Type
- single nucleotide variant
- Location
- chr9:137142141 (GRCh38)
- Structure
- AlphaFold pLDDT 44.02
- Residue 129
- the 'disordered' region
Similar variants
- GRIN1 p.Arg659Gln Pathogenic/Likely pathogenic ★★ same condition
- GRIN1 p.Arg659Trp Pathogenic ★★ same condition
- GRIN1 p.Arg794Gln Pathogenic/Likely pathogenic ★★ ⚠ same condition
- GRIN1 p.Arg844Cys Pathogenic/Likely pathogenic ★★ same condition
- GRIN1 p.Arg844Leu Pathogenic/Likely pathogenic ★★ same condition
- GRIN1 p.Asp227His Likely pathogenic ★★ same condition
- GRIN1 p.Asp732Glu Pathogenic/Likely pathogenic ★★ same condition
- GRIN1 p.Gly618Arg Likely pathogenic ★★ same condition
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/grin1-p-ser129 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown