ALG11 p.Glu431=
c.1293A>G · rs1211890444 · VCV740821
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0517%, 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 -0.041 | GERP 0.58, phastCons 0.001 |
| Overall | ||
| CADD | 6.33 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0517%
Admixed American · 31/60,006 alleles
Filtering AF
0.0374%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0325%
Overall
0.00211%
34/1,614,072 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0517% | 1,936 |
| European (non-Finnish) | 0.000254% | 393,340 |
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
- ALG11
- Protein
- p.Glu431=
- Coding
- c.1293A>G
- MANE Select
- NM_001004127
- dbSNP
- rs1211890444
- Type
- single nucleotide variant
- Location
- chr13:52028404 (GRCh38)
- Gene constraint
- LOEUF 0.908 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.40
Similar variants
- ALG11 p.Glu431Lys Uncertain significance ★ ⚠ same residue
- ALG11 c.45-2A>T Likely pathogenic ★★ same type
- ALG11 p.Arg468Cys Likely pathogenic ★★ ⚠ same type
- ALG11 p.Arg468His Likely pathogenic ★★ same type
- ALG11 p.Met1Val Likely pathogenic ★★ same type
- ALG11 c.*540T>A Uncertain significance ★★ ⚠ same type
- ALG11 p.Arg136Cys Uncertain significance ★★ same type
- ALG11 p.Arg15Thr 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/alg11-p-glu431 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown