ODC1 p.Pro423=
c.1269C>T · rs1049500 · VCV1280616
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 54.5%, eas) — too common for a highly-penetrant pathogenic allele
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 -2.1 | GERP -3.9 |
| Overall | ||
| CADD | 3.59 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
54.5%
East Asian · 24,471/44,866 alleles
Filtering AF
54%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 53.7%
Overall
8.05%
129,880/1,613,840 alleles · common
exomes 109,383/1,461,794 · genomes 20,497/152,046 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 54.5% | 2 |
| African / African-American | 25.2% | 4 |
| South Asian | 21.4% | 5 |
| Admixed American | 13% | 8 |
| Finnishnot grpmax-eligible | 11.4% | 9 |
| Remaining individualsnot grpmax-eligible | 10.1% | 10 |
| Middle Eastern | 7.79% | 13 |
| Ashkenazi Jewishnot grpmax-eligible | 4.63% | 22 |
| European (non-Finnish) | 3.71% | 27 |
| Amishnot grpmax-eligible | 0.44% | 228 |
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.Pro423=
- Coding
- c.1269C>T
- MANE Select
- NM_002539
- dbSNP
- rs1049500
- Type
- single nucleotide variant
- Location
- chr2:10440841 (GRCh38)
- Gene constraint
- LOEUF 0.617 · pLI 0.23 (gnomAD)
- Structure
- AlphaFold pLDDT 88.30 · 11 PDB
- Residue 423
- a UniProt-annotated variant site (in babs)
Similar variants
- 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 c.914-1G>C Likely pathogenic ★ same type
- ODC1 p.Gln418Ter 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/odc1-p-pro423 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown