GORAB p.Lys137Ter
c.409A>T · rs2101821379 · VCV2870262
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 2 of 5 |
| Splicing | ||
| SpliceAI | Δ1.00 | donor gain · deltas |
| Pangolin | Δ0.86 | gain · loss 0.12 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 9.4 | GERP 1.6, phastCons 1 |
| Overall | ||
| CADD | 49.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- GORAB
- Protein
- p.Lys137Ter
- Coding
- c.409A>T
- MANE Select
- NM_152281
- dbSNP
- rs2101821379
- Type
- single nucleotide variant
- Location
- chr1:170539557 (GRCh38)
- Gene constraint
- LOEUF 0.802 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 71.86
Similar variants
- GORAB p.Lys137Glu Uncertain significance ★ same residue
- GORAB p.Lys137fs Pathogenic/Likely pathogenic ★★ same residue
- GORAB c.420-2A>T Pathogenic/Likely pathogenic ★★ same type
- GORAB p.Arg262Ter Pathogenic/Likely pathogenic ★★ same type
- GORAB p.Arg35Ter Pathogenic ★★ same type
- GORAB p.Arg40Ter Pathogenic/Likely pathogenic ★★ same type
- GORAB p.Gln64Ter Pathogenic ★★ same type
- GORAB p.Trp5Ter Pathogenic/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/gorab-p-lys137ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown