ARSB c.690+16A>C
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
mucopolysaccharidosis type 6
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +16 | near-intronic (+16 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.12 | GERP -0.98, phastCons 0.001 |
| Non-coding constraint | Z 1.28 | 1 kb window · o/e 0.90 · regional · uncalibrated |
| Overall | ||
| CADD | 3.526 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- ARSB
- Coding
- c.690+16A>C
- MANE Select
- NM_000046
- dbSNP
- rs549166442
- Type
- single nucleotide variant
- Location
- chr5:78964400 (GRCh38)
- Gene constraint
- LOEUF 1.032 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.74 · 1 PDB
Disease context
mucopolysaccharidosis type 6 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Mucopolysaccharidosis type 6 (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Childhood
- Prevalence
- 1-9 / 1 000 000 (Europe)
Similar variants
- ARSB c.1142+1G>A Pathogenic ★★ same condition
- ARSB c.1142+1G>T Pathogenic ★★ same condition
- ARSB c.1142+2T>A Pathogenic/Likely pathogenic ★★ same condition
- ARSB c.1142+2T>C Pathogenic ★★ same condition
- ARSB c.1143-1G>A Pathogenic/Likely pathogenic ★★ same condition
- ARSB c.1143-1G>C Pathogenic ★★ same condition
- ARSB c.1143-8T>G Pathogenic/Likely pathogenic ★★ same condition
- ARSB c.1213+6T>C 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/arsb-c-690-plus-16a-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown