ODC1 p.Ser309=
c.927G>A · rs778262198 · VCV2582976
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
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 -8.4 | GERP -3.5 |
| Overall | ||
| CADD | 0.94 | 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
0.0092%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00735%
Overall
0.00242%
39/1,614,066 alleles · ultra-rare
exomes 33/1,461,766 · genomes 6/152,300 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,062 |
| South Asian | 0.0154% | 6,505 |
| East Asian | 0.00891% | 11,222 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,504 |
| European (non-Finnish) | 0.00153% | 65,554 |
| African / African-American | 0.00133% | 75,032 |
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
- ODC1
- Protein
- p.Ser309=
- Coding
- c.927G>A
- MANE Select
- NM_002539
- dbSNP
- rs778262198
- Type
- single nucleotide variant
- Location
- chr2:10441916 (GRCh38)
- Gene constraint
- LOEUF 0.617 · pLI 0.23 (gnomAD)
- Structure
- AlphaFold pLDDT 88.30 · 11 PDB
Similar variants
- ODC1 p.Ser309Leu Likely benign same residue
- ODC1 c.1242-2A>G Pathogenic ★★ same type
- ODC1 p.Ile251Met Uncertain significance ★★ ⚠ same type
- ODC1 p.Pro264Leu Uncertain significance ★★ ⚠ same type
- ODC1 p.Ala258Val Likely benign ★★ same type
- ODC1 p.Gly253Arg Benign/Likely benign ★★ same type
- ODC1 p.Gly84Arg Likely benign ★★ ⚠ same type
- ODC1 p.Pro423= Benign ★★ 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/odc1-p-ser309 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown