ALG1 c.390+13C>A
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.4%, afr)
Conditions
1
ALG1-congenital disorder of glycosylation
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +13 | near-intronic (+13 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.89 | GERP -2.8 |
| Overall | ||
| CADD | 0.996 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.4%
African / African-American · 1,793/74,850 alleles
Filtering AF
2.3%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.27%
Overall
0.127%
2,050/1,609,738 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.4% | 42 |
| Admixed American | 0.195% | 513 |
| Remaining individualsnot grpmax-eligible | 0.157% | 636 |
| Middle Eastern | 0.0345% | 2,900 |
| European (non-Finnish) | 0.00323% | 30,961 |
| South Asian | 0.0022% | 45,477 |
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
- ALG1
- Coding
- c.390+13C>A
- MANE Select
- NM_019109
- dbSNP
- rs62036244
- Type
- single nucleotide variant
- Location
- chr16:5073269 (GRCh38)
- Gene constraint
- LOEUF 1.419 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 93.24
Disease context
ALG1-congenital disorder of glycosylation — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor ALG1-CDG (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Infancy, Neonatal
Similar variants
- ALG1 c.1187+1G>A Pathogenic/Likely pathogenic ★★ same condition
- ALG1 c.1187+2T>C Pathogenic ★★ same condition
- ALG1 c.1188-2A>G Pathogenic/Likely pathogenic ★★ same condition
- ALG1 c.209-2A>G Likely pathogenic ★★ same condition
- ALG1 c.539+1G>A Pathogenic/Likely pathogenic ★★ same condition
- ALG1 c.630-2A>G Likely pathogenic ★★ same condition
- ALG1 c.863-2A>G Likely pathogenic ★★ same condition
- ALG1 c.961+1G>A 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/alg1-c-390-plus-13c-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown