ALG9 p.Tyr158=
c.474C>T · rs1555151653 · VCV512411
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,544,266)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.33 | donor loss, 2 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.2 | GERP -3.5, phastCons 1 |
| Overall | ||
| CADD | 12.21 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,544,266). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- ALG9
- Protein
- p.Tyr158=
- Coding
- c.474C>T
- MANE Select
- NM_024740
- dbSNP
- rs1555151653
- Type
- single nucleotide variant
- Location
- chr11:111865183 (GRCh38)
- Gene constraint
- LOEUF 0.853 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.35 · 2 PDB
Similar variants
- ALG9 c.566-1G>A Pathogenic/Likely pathogenic ★★ same type
- ALG9 c.896-2A>G Likely pathogenic ★★ same type
- ALG9 p.Arg143Ter Pathogenic/Likely pathogenic ★★ same type
- ALG9 p.Trp248Ter Pathogenic/Likely pathogenic ★★ same type
- ALG9 p.Tyr287Cys Pathogenic/Likely pathogenic ★★ same type
- ALG9 c.*1607C>T Uncertain significance ★★ same type
- ALG9 c.*1624A>C Uncertain significance ★★ same type
- ALG9 c.*1722C>T 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/alg9-p-tyr158 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown