ALS2 p.Ile470=
c.1410C>T · VCV3772586
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, 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 5 | GERP 1, phastCons 1 |
| Overall | ||
| CADD | 9.054 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,180,002 alleles
Overall
6.84e-05%
1/1,461,768 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
- ALS2
- Protein
- p.Ile470=
- Coding
- c.1410C>T
- MANE Select
- NM_020919
- Type
- single nucleotide variant
- Location
- chr2:201757463 (GRCh38)
- Gene constraint
- LOEUF 0.649 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 74.69
- Residue 470
- the 'disordered' region
Similar variants
- ALS2 c.1640+1G>A Pathogenic/Likely pathogenic ★★ same type
- ALS2 c.2580+2T>C Pathogenic ★★ same type
- ALS2 c.3703-2A>G Pathogenic/Likely pathogenic ★★ same type
- ALS2 c.4626+1G>A Pathogenic/Likely pathogenic ★★ same type
- ALS2 p.Ala573Glu Likely pathogenic ★★ same type
- ALS2 p.Arg1139Ter Pathogenic/Likely pathogenic ★★ same type
- ALS2 p.Arg1421Ter Pathogenic/Likely pathogenic ★★ same type
- ALS2 p.Arg1461Ter Pathogenic ★★ 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/als2-p-ile470 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown