ALG1 p.Lys336Asn
c.1008G>C · VCV4269965
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
ambiguous
0.4419 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| AlphaMissense | 0.4419 | ambiguous |
|---|---|---|
| REVEL | 0.403 | indeterminate |
| SaProt | LLR -10.58 | damaging |
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.29 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP 5.1 | GERP 1.8, phastCons 1 |
| Regional constraint | o/e 1.27 | unconstrained · MANE · 13 kb · p 3.2e-11 · regional, not allelic |
| Overall | ||
| CADD | 21.9 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
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
- ALG1
- Protein
- p.Lys336Asn
- Coding
- c.1008G>C
- MANE Select
- NM_019109
- Type
- single nucleotide variant
- Location
- chr16:5080992 (GRCh38)
- Gene constraint
- LOEUF 1.419 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 93.24
Similar variants
- ALG1 p.Lys336Gln Uncertain significance ★ ⚠ same residue
- ALG1 p.Ala360Val Pathogenic/Likely pathogenic ★★ same condition
- ALG1 p.Gln342Pro Pathogenic/Likely pathogenic ★★ ⚠ same condition
- ALG1 p.Ala278Thr Uncertain significance ★★ ⚠ same condition
- ALG1 p.Arg257Gln Uncertain significance ★★ ⚠ same condition
- ALG1 p.Asn311Lys Uncertain significance ★★ ⚠ same condition
- ALG1 p.Asn80His Uncertain significance ★★ ⚠ same condition
- ALG1 p.Asp252Glu Uncertain significance ★★ ⚠ same condition
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/alg1-p-lys336asn (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown