ODC1 p.Ala156=
c.468C>T · rs774367424 · VCV2650674
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00333%, amr)
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 0.11 | GERP -2.7, phastCons 0.73 |
| Overall | ||
| CADD | 9.337 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00333%
Admixed American · 2/59,990 alleles
Filtering AF
0.00196%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00168%
Overall
0.00211%
34/1,613,912 alleles · very rare
exomes 29/1,461,760 · genomes 5/152,152 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00333% | 29,995 |
| European (non-Finnish) | 0.00271% | 36,873 |
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.Ala156=
- Coding
- c.468C>T
- MANE Select
- NM_002539
- dbSNP
- rs774367424
- Type
- single nucleotide variant
- Location
- chr2:10443818 (GRCh38)
- Gene constraint
- LOEUF 0.617 · pLI 0.23 (gnomAD)
- Structure
- AlphaFold pLDDT 88.30 · 11 PDB
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 p.Pro423= Benign ★★ same type
- ODC1 c.914-1G>C 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-ala156 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown