GRIN2B p.Ser896=
c.2688C>A · rs201445433 · VCV3234131
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000763%, nfe)
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 3.8 | GERP 0.63, phastCons 1 |
| Overall | ||
| CADD | 8.591 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000763%
European (non-Finnish) · 9/1,180,006 alleles
Filtering AF
0.000359%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00026%
Overall
0.000558%
9/1,614,142 alleles · very rare
exomes 9/1,461,822 · genomes 0/152,320 · 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
- GRIN2B
- Protein
- p.Ser896=
- Coding
- c.2688C>A
- MANE Select
- NM_000834
- dbSNP
- rs201445433
- Type
- single nucleotide variant
- Location
- chr12:13564550 (GRCh38)
- Gene constraint
- LOEUF 0.102 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 60.66 · 36 PDB
Similar variants
- GRIN2B c.2172-2A>G Pathogenic ★★ same type
- GRIN2B p.Ala639Val Pathogenic/Likely pathogenic ★★ same type
- GRIN2B p.Ala644Asp Pathogenic ★★ same type
- GRIN2B p.Ala734Val Likely pathogenic ★★ same type
- GRIN2B p.Ala819Thr Pathogenic/Likely pathogenic ★★ same type
- GRIN2B p.Arg1111His Pathogenic/Likely pathogenic ★★ ⚠ same type
- GRIN2B p.Arg393Ter Pathogenic/Likely pathogenic ★★ same type
- GRIN2B p.Arg519Gln Likely pathogenic ★★ 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/grin2b-p-ser896 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown