GABBR2 p.Phe670=
c.2010C>T · rs950764173 · VCV2990577
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00334%, amr)
Conditions
1
Epileptic encephalopathy
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.32 | acceptor gain · deltas |
|---|---|---|
| Pangolin | Δ0.36 | gain · loss 0.19 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 1.5 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 18.6 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00334%
Admixed American · 2/59,958 alleles
Filtering AF
0.000553%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000207%
Overall
0.000186%
3/1,610,904 alleles · very rare
exomes 3/1,458,624 · genomes 0/152,280 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00334% | 29,979 |
| European (non-Finnish) | 8.49e-05% | 1,177,277 |
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
- GABBR2
- Protein
- p.Phe670=
- Coding
- c.2010C>T
- MANE Select
- NM_005458
- dbSNP
- rs950764173
- Type
- single nucleotide variant
- Location
- chr9:98306340 (GRCh38)
- Gene constraint
- LOEUF 0.394 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 78.00 · 26 PDB
- Residue 670
- an α-helix
Similar variants
- GABBR2 p.Phe670Leu Uncertain significance ★ ⚠ same residue
- GABBR2 p.Gly693Trp Pathogenic ★★ same condition
- GABBR2 p.Ala444Thr Uncertain significance ★★ ⚠ same condition
- GABBR2 p.Ala580Ser Uncertain significance ★★ ⚠ same condition
- GABBR2 p.Ala69Pro Uncertain significance ★★ ⚠ same condition
- GABBR2 p.Ala708Ser Uncertain significance ★★ ⚠ same condition
- GABBR2 p.Arg301His Uncertain significance ★★ ⚠ same condition
- GABBR2 p.Arg48Trp Uncertain significance ★★ ⚠ 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/gabbr2-p-phe670 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown