ALG9 p.Tyr401=
c.1203C>T · rs1555119896 · VCV514612
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.45 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.9 | GERP 0.066, phastCons 1 |
| Overall | ||
| CADD | 7.429 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- ALG9
- Protein
- p.Tyr401=
- Coding
- c.1203C>T
- MANE Select
- NM_024740
- dbSNP
- rs1555119896
- Type
- single nucleotide variant
- Location
- chr11:111838370 (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-tyr401 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown