Is IDS p.Ser117del (c.349_351del) pathogenic?

IDS p.Ser117del (c.349351del) is classified Pathogenic in IDS (ClinVar, Single submitter, 2 submitters; last evaluated 2024-06-07). No gnomAD frequency available for this variant; Associated with mucopolysaccharidosis type 2.

What condition is associated with IDS p.Ser117del (c.349_351del)?

IDS p.Ser117del (c.349_351del) is associated with mucopolysaccharidosis type 2 (ClinVar).

How common is IDS p.Ser117del (c.349_351del) in the general population?

IDS p.Ser117del (c.349_351del) is no gnomAD frequency available for this variant (gnomAD).

How is Mucopolysaccharidosis type 2 inherited?

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

IDS p.Ser117del

c.349_351del · rs483352905 · VCV10501

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

mucopolysaccharidosis type 2

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 4.9	GERP 1.1, phastCons 1
Region caveats
Repeat context	seg dup	· reads may not map uniquely · confidence, not pathogenicity

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: IDS
Protein: p.Ser117del
Coding: c.349_351del
MANE Select: NM_000202
dbSNP: rs483352905
Type: Deletion
Location: chrX:149503379 (GRCh38)
Structure: AlphaFold pLDDT 93.39 · 2 PDB
Residue 117: a UniProt-annotated variant site (in mps2; severe form); a UniProt-annotated variant site (in mps2; severe form; deleterious mutation; results in an inactive enzyme)

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

Disease context

mucopolysaccharidosis type 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Mucopolysaccharidosis type 2 (Orphanet):

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

Similar variants

IDS p.Ser117Tyr Likely pathogenic ★ same residue
IDS c.418+1_418+4del Pathogenic ★★ same condition
IDS p.Arg468fs Pathogenic/Likely pathogenic ★★ same condition
IDS p.Arg8fs Pathogenic ★★ same condition
IDS p.Arg96del Likely pathogenic ★★ same condition
IDS p.Asn280fs Pathogenic ★★ same condition
IDS p.Asp319fs Pathogenic ★★ same condition
IDS p.Gln474fs 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/ids-p-ser117del (accessed [today's date]).

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