ALX3 p.Arg209=
c.627G>A · rs113851340 · VCV259986
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.617%, afr)
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 3.3 | GERP -1.1, phastCons 1 |
| Overall | ||
| CADD | 17.57 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.617%
African / African-American · 463/75,052 alleles
Filtering AF
0.57%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.552%
Overall
0.0333%
538/1,614,202 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.617% | 162 |
| Remaining individualsnot grpmax-eligible | 0.072% | 1,389 |
| Middle Eastern | 0.0495% | 2,021 |
| Admixed American | 0.03% | 3,335 |
| South Asian | 0.00439% | 22,772 |
| European (non-Finnish) | 0.000424% | 236,005 |
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
- ALX3
- Protein
- p.Arg209=
- Coding
- c.627G>A
- MANE Select
- NM_006492
- dbSNP
- rs113851340
- Type
- single nucleotide variant
- Location
- chr1:110061531 (GRCh38)
- Gene constraint
- LOEUF 1.051 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 62.90
- Residue 209
- a DNA-binding region
Similar variants
- ALX3 p.Pro250Leu Uncertain significance ★★ ⚠ same type
- ALX3 p.Pro40Ala Uncertain significance ★★ ⚠ same type
- ALX3 p.Ser131Arg Uncertain significance ★★ ⚠ same type
- ALX3 p.Tyr320Cys Uncertain significance ★★ ⚠ same type
- ALX3 c.277+33C>T Benign ★★ same type
- ALX3 p.Pro138= Benign/Likely benign ★★ same type
- ALX3 p.Pro250Ala Benign/Likely benign ★★ same type
- ALX3 p.Pro305= 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/alx3-p-arg209 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown