ALX1 p.Ser210=
c.630A>T · rs115409839 · VCV788436
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.63%, 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 -0.026 | GERP -1, phastCons 0.03 |
| Overall | ||
| CADD | 6.573 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.63%
African / African-American · 1,972/74,950 alleles
Filtering AF
2.53%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.5%
Overall
0.142%
2,282/1,612,246 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.63% | 38 |
| Admixed American | 0.234% | 428 |
| Remaining individualsnot grpmax-eligible | 0.167% | 600 |
| Middle Eastern | 0.0991% | 1,009 |
| South Asian | 0.00549% | 18,204 |
| European (non-Finnish) | 0.00458% | 21,826 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00339% | 29,524 |
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
- ALX1
- Protein
- p.Ser210=
- Coding
- c.630A>T
- MANE Select
- NM_006982
- dbSNP
- rs115409839
- Type
- single nucleotide variant
- Location
- chr12:85286951 (GRCh38)
- Gene constraint
- LOEUF 0.838 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.32
- Residue 210
- the 'transactivation domain' region
Similar variants
- ALX1 p.Arg257Pro Uncertain significance ★★ ⚠ same type
- ALX1 p.Val50Ala Uncertain significance ★★ ⚠ same type
- ALX1 c.532-17T>C Benign/Likely benign ★★ same type
- ALX1 c.660+17A>G Benign/Likely benign ★★ same type
- ALX1 p.Ala199= Benign/Likely benign ★★ same type
- ALX1 p.His61Arg Benign ★★ same type
- ALX1 p.His89Arg Benign ★★ same type
- ALX1 p.Leu119= Likely 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/alx1-p-ser210 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown