Is ARSB p.Ala39fs (c.116_123del) pathogenic?

ARSB p.Ala39fs (c.116123del) is classified Pathogenic in ARSB (ClinVar, Multiple submitters, 3 submitters; last evaluated 2018-01-01). Absent from gnomAD; Associated with mucopolysaccharidosis type 6.

What condition is associated with ARSB p.Ala39fs (c.116_123del)?

ARSB p.Ala39fs (c.116_123del) is associated with mucopolysaccharidosis type 6 (ClinVar).

How common is ARSB p.Ala39fs (c.116_123del) in the general population?

ARSB p.Ala39fs (c.116_123del) is absent from gnomAD (gnomAD).

How is Mucopolysaccharidosis type 6 inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

ARSB p.Ala39fs

c.116_123del · rs1554032243 · VCV495377

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

mucopolysaccharidosis type 6

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function; NMD-escape possible for C-terminal truncations
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -2.6	GERP -2.6

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: ARSB
Protein: p.Ala39fs
Coding: c.116_123del
MANE Select: NM_020427 · reported on NM_000046
dbSNP: rs1554032243
Type: Deletion
Location: chr5:78985126 (GRCh38)
Structure: AlphaFold pLDDT 84.32 · 2 PDB
Residue 39: the upar/ly6 domain; a disulfide bond

Full ARSB gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

mucopolysaccharidosis type 6 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Mucopolysaccharidosis type 6 (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood
Prevalence: 1-9 / 1 000 000 (Europe)

Similar variants

ARSB p.Ala39= Likely benign ★ same residue
ARSB p.Gly38fs Pathogenic/Likely pathogenic ★★ same condition
ARSB p.Gly40fs Pathogenic/Likely pathogenic ★★ same condition
ARSB p.Leu354fs Pathogenic/Likely pathogenic ★★ same condition
ARSB p.Pro248fs Pathogenic ★★ same condition
ARSB p.Ser37fs Pathogenic/Likely pathogenic ★★ same condition
ARSB p.Thr526fs Pathogenic ★★ same condition
ARSB p.Val143fs 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-p-ala39fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown