ALG11 p.Leu268=
c.804A>G · rs141470932 · VCV791693
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00439%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.3 | GERP -3.7, phastCons 0.96 |
| Overall | ||
| CADD | 7.659 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00439%
South Asian · 4/91,088 alleles
Filtering AF
0.00215%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00191%
Overall
0.0026%
42/1,614,102 alleles · very rare
exomes 40/1,461,874 · genomes 2/152,228 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00439% | 22,772 |
| European (non-Finnish) | 0.00297% | 33,716 |
| East Asian | 0.00223% | 44,892 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,486 |
| African / African-American | 0.00133% | 74,936 |
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
- ALG11
- Protein
- p.Leu268=
- Coding
- c.804A>G
- MANE Select
- NM_001004127
- dbSNP
- rs141470932
- Type
- single nucleotide variant
- Location
- chr13:52024534 (GRCh38)
- Gene constraint
- LOEUF 0.908 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.40
Similar variants
- ALG11 p.Leu268Ile Uncertain significance ★★ ⚠ same residue
- ALG11 c.45-2A>T Likely pathogenic ★★ same type
- ALG11 p.Arg468Cys Likely pathogenic ★★ ⚠ same type
- ALG11 p.Arg468His Likely pathogenic ★★ same type
- ALG11 p.Met1Val Likely pathogenic ★★ same type
- ALG11 c.*540T>A Uncertain significance ★★ ⚠ same type
- ALG11 p.Arg136Cys Uncertain significance ★★ same type
- ALG11 p.Arg15Thr 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/alg11-p-leu268 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown