ALG9 p.Ala73=
c.219T>C · rs782407372 · VCV507141
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00136%, nfe)
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 1.4 | GERP -0.74, phastCons 1 |
| Overall | ||
| CADD | 11.51 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00136%
European (non-Finnish) · 16/1,179,526 alleles
Filtering AF
0.000803%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00065%
Overall
0.000992%
16/1,612,306 alleles · very rare
exomes 15/1,461,062 · genomes 1/151,244 · joint denominator
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
- ALG9
- Protein
- p.Ala73=
- Coding
- c.219T>C
- MANE Select
- NM_024740
- dbSNP
- rs782407372
- Type
- single nucleotide variant
- Location
- chr11:111870283 (GRCh38)
- Gene constraint
- LOEUF 0.853 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.35 · 2 PDB
Similar variants
- ALG9 p.Ala73Val Uncertain significance ★ ⚠ same residue
- 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
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-ala73 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown