ALG6 c.346+15G>T
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.51e-05%, nfe)
Conditions
1
ALG6-congenital disorder of glycosylation 1C
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +15 | near-intronic (+15 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.62 | GERP -1.6 |
| Non-coding constraint | Z 2.00 | 1 kb window · o/e 0.84 · regional · uncalibrated |
| Overall | ||
| CADD | 3.268 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.51e-05%
European (non-Finnish) · 1/1,175,400 alleles
Overall
6.86e-05%
1/1,456,714 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
- ALG6
- Coding
- c.346+15G>T
- MANE Select
- NM_013339
- dbSNP
- rs2523729976
- Type
- single nucleotide variant
- Location
- chr1:63404556 (GRCh38)
- Gene constraint
- LOEUF 0.892 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 93.08
Disease context
ALG6-congenital disorder of glycosylation 1C — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor ALG6-CDG (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Infancy, Neonatal
Similar variants
- ALG6 c.1128-1G>A Likely pathogenic ★★ same condition
- ALG6 c.1128-2A>C Likely pathogenic ★★ same condition
- ALG6 c.1326+1G>A Pathogenic/Likely pathogenic ★★ same condition
- ALG6 c.257+5G>A Pathogenic/Likely pathogenic ★★ same condition
- ALG6 c.429+1G>T Likely pathogenic ★★ same condition
- ALG6 c.495-2A>G Likely pathogenic ★★ same condition
- ALG6 c.495-2A>T Likely pathogenic ★★ same condition
- ALG6 c.680+1G>A Pathogenic/Likely pathogenic ★★ 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/alg6-c-346-plus-15g-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown