ALG6 c.429+46T>C
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.07%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +46 | near-intronic (+46 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.006 | GERP -0.73 |
| Non-coding constraint | Z 1.82 | 1 kb window · o/e 0.84 · regional · uncalibrated |
| Overall | ||
| CADD | 8.647 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.07%
African / African-American · 779/72,672 alleles
Filtering AF
1.01%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.985%
Overall
0.074%
1,111/1,501,706 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.07% | 93 |
| Admixed American | 0.246% | 406 |
| Remaining individualsnot grpmax-eligible | 0.121% | 826 |
| Middle Eastern | 0.0965% | 1,037 |
| European (non-Finnish) | 0.00982% | 10,186 |
| South Asian | 0.00338% | 29,563 |
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.429+46T>C
- MANE Select
- NM_013339
- dbSNP
- rs138180242
- Type
- single nucleotide variant
- Location
- chr1:63406445 (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.1128-1G>A Likely pathogenic ★★ same type
- ALG6 c.1128-2A>C Likely pathogenic ★★ same type
- ALG6 c.1326+1G>A Pathogenic/Likely pathogenic ★★ same type
- ALG6 c.257+5G>A Pathogenic/Likely pathogenic ★★ same type
- ALG6 c.429+1G>T Likely pathogenic ★★ same type
- ALG6 c.495-2A>G Likely pathogenic ★★ same type
- ALG6 c.495-2A>T Likely pathogenic ★★ same type
- ALG6 c.680+1G>A 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-c-429-plus-46t-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown