Is SGSH p.Phe362fs (c.1085_1086del) pathogenic?

SGSH p.Phe362fs (c.10851086del) is classified Likely pathogenic in SGSH (ClinVar, Single submitter, 1 submitter; last evaluated 2023-04-24). No gnomAD frequency available for this variant; Associated with mucopolysaccharidosis type 3A.

What condition is associated with SGSH p.Phe362fs (c.1085_1086del)?

SGSH p.Phe362fs (c.1085_1086del) is associated with mucopolysaccharidosis type 3A (ClinVar).

How common is SGSH p.Phe362fs (c.1085_1086del) in the general population?

SGSH p.Phe362fs (c.1085_1086del) is no gnomAD frequency available for this variant (gnomAD).

How is Mucopolysaccharidosis type 3 inherited?

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

SGSH p.Phe362fs

c.1085_1086del · rs2510860466 · VCV2678725

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

mucopolysaccharidosis type 3A

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	escapes	premature termination codon in the last exon (8 of 8) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.94	GERP -2.3, phastCons 0.42

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: SGSH
Protein: p.Phe362fs
Coding: c.1085_1086del
MANE Select: NM_000199
dbSNP: rs2510860466
Type: Deletion
Location: chr17:80210875 (GRCh38)
Gene constraint: LOEUF 1.26 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 96.64 · 2 PDB
Residue 362: a β-strand

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

Disease context

mucopolysaccharidosis type 3A — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Mucopolysaccharidosis type 3 (Orphanet):

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

Similar variants

SGSH p.Phe362Val Uncertain significance ★★ ⚠ same residue
SGSH p.Ala231fs Pathogenic/Likely pathogenic ★★ same condition
SGSH p.Ala232fs Pathogenic/Likely pathogenic ★★ same condition
SGSH p.Arg385fs Pathogenic/Likely pathogenic ★★ same condition
SGSH p.Asn151fs Likely pathogenic ★★ same condition
SGSH p.Gln449fs Pathogenic/Likely pathogenic ★★ same condition
SGSH p.His476fs Pathogenic/Likely pathogenic ★★ same condition
SGSH p.Leu17fs 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/sgsh-p-phe362fs (accessed [today's date]).

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