ALG6 p.Cys303del
c.908_910del · rs1057517952 · VCV372732
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00163%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 5.1 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 16.0 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00163%
European (non-Finnish) · 19/1,168,342 alleles
Filtering AF
0.00104%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000838%
Overall
0.00125%
20/1,600,196 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00163% | 61,492 |
| Remaining individualsnot grpmax-eligible | 0.00162% | 61,888 |
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
- ALG6
- Protein
- p.Cys303del
- Coding
- c.908_910del
- MANE Select
- NM_013339
- dbSNP
- rs1057517952
- Type
- Deletion
- Location
- chr1:63415876 (GRCh38)
- Gene constraint
- LOEUF 0.892 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 93.08
Similar variants
- ALG6 c.82_82+8del Likely pathogenic ★★ same type
- ALG6 p.Asn283fs Pathogenic/Likely pathogenic ★★ same type
- ALG6 p.Gln417fs Pathogenic/Likely pathogenic ★★ same type
- ALG6 p.Leu416fs Pathogenic/Likely pathogenic ★★ same type
- ALG6 p.Met34fs Pathogenic/Likely pathogenic ★★ same type
- ALG6 p.Phe228fs Pathogenic/Likely pathogenic ★★ same type
- ALG6 p.Phe336fs Pathogenic/Likely pathogenic ★★ same type
- ALG6 p.Pro379fs Pathogenic/Likely 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/alg6-p-cys303del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown