OAT p.Lys405=
c.1215G>A · rs2494427962 · VCV2709937
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
ornithine aminotransferase deficiency
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 2.5 | GERP 0.98, phastCons 1 |
| Overall | ||
| CADD | 12.84 | PHRED · no single calibrated threshold — expert panels disagree |
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
- OAT
- Protein
- p.Lys405=
- Coding
- c.1215G>A
- MANE Select
- NM_000274
- dbSNP
- rs2494427962
- Type
- single nucleotide variant
- Location
- chr10:124398047 (GRCh38)
- Gene constraint
- LOEUF 0.968 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.29 · 35 PDB
- Residue 405
- a modified residue (n6-acetyllysine; alternate); a modified residue (n6-succinyllysine; alternate); a β-strand
Disease context
ornithine aminotransferase deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Gyrate atrophy of choroid and retina (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Childhood
- Prevalence
- 1-9 / 100 000 (Finland)
Similar variants
- OAT c.1014+1G>A Likely pathogenic ★★ same condition
- OAT c.199+2T>A Likely pathogenic ★★ same condition
- OAT c.425-2A>G Pathogenic ★★ same condition
- OAT c.520+1G>A Likely pathogenic ★★ same condition
- OAT c.648+1G>A Likely pathogenic ★★ same condition
- OAT c.772-1G>A Pathogenic/Likely pathogenic ★★ same condition
- OAT c.900+1G>A Pathogenic/Likely pathogenic ★★ same condition
- OAT p.Arg180Thr Pathogenic/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/oat-p-lys405 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown