ALG6 p.Phe49fs
c.147del · rs756566938 · VCV2748650
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
ultra-rare (gnomAD MAF 6.701e-06)
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. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 3 of 15 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7.5 | GERP 2.7, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
dbSNP / gnomAD
Global frequency
0.00067%
via dbSNP · ultra-rare
No ancestry breakdown or filtering allele frequency is available for this variant, so BA1/BS1 cannot be assessed from this figure alone.
Variant & gene context
- Gene
- ALG6
- Protein
- p.Phe49fs
- Coding
- c.147del
- MANE Select
- NM_013339
- dbSNP
- rs756566938
- Type
- Deletion
- Location
- chr1:63396574 (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.82_82+8del Likely pathogenic ★★ same condition
- ALG6 p.Asn283fs Pathogenic/Likely pathogenic ★★ same condition
- ALG6 p.Gln417fs Pathogenic/Likely pathogenic ★★ same condition
- ALG6 p.Leu416fs Pathogenic/Likely pathogenic ★★ same condition
- ALG6 p.Met34fs Pathogenic/Likely pathogenic ★★ same condition
- ALG6 p.Phe228fs Pathogenic/Likely pathogenic ★★ same condition
- ALG6 p.Phe336fs Pathogenic/Likely pathogenic ★★ same condition
- ALG6 p.Pro379fs 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-p-phe49fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown