ODAD3 p.Val229=
c.687G>C · rs1464668370 · VCV743808
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000509%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.17 | GERP -4.4, phastCons 0.3 |
| Overall | ||
| CADD | 4.466 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000509%
European (non-Finnish) · 6/1,179,898 alleles
Filtering AF
0.000183%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00012%
Overall
0.000372%
6/1,613,792 alleles · very rare
exomes 4/1,461,630 · genomes 2/152,162 · joint denominator
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
- ODAD3
- Protein
- p.Val229=
- Coding
- c.687G>C
- MANE Select
- NM_145045
- dbSNP
- rs1464668370
- Type
- single nucleotide variant
- Location
- chr19:11426710 (GRCh38)
- Gene constraint
- LOEUF 1.019 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.97 · 1 PDB
Similar variants
- ODAD3 c.964-1G>A Likely pathogenic ★★ same type
- ODAD3 p.Gln354Ter Pathogenic ★★ same type
- ODAD3 c.1435-5C>A Uncertain significance ★★ same type
- ODAD3 p.Ala203Pro Uncertain significance ★★ ⚠ same type
- ODAD3 p.Ala220Val Uncertain significance ★★ ⚠ same type
- ODAD3 p.Ala308Thr Uncertain significance ★★ ⚠ same type
- ODAD3 p.Ala341Ser Uncertain significance ★★ ⚠ same type
- ODAD3 p.Ala432Thr Uncertain significance ★★ ⚠ 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/odad3-p-val229 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown