ALG11 p.Ser258=
c.774T>G · rs1593903249 · VCV745757
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, 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 0.047 | GERP -0.6, phastCons 0.97 |
| Overall | ||
| CADD | 7.041 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/60,016 alleles
Overall
0.000657%
1/152,250 alleles · very rare
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.Ser258=
- Coding
- c.774T>G
- MANE Select
- NM_001004127
- dbSNP
- rs1593903249
- Type
- single nucleotide variant
- Location
- chr13:52024504 (GRCh38)
- Gene constraint
- LOEUF 0.908 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.40
Similar variants
- ALG11 p.Ser258Cys 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-ser258 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown