Is IDS p.Ser69Ter (c.205_206insAAACTGGCAT) pathogenic?

IDS p.Ser69Ter (c.205206insAAACTGGCAT) 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.Ser69Ter (c.205_206insAAACTGGCAT)?

IDS p.Ser69Ter (c.205_206insAAACTGGCAT) is associated with mucopolysaccharidosis type 2 (ClinVar).

How common is IDS p.Ser69Ter (c.205_206insAAACTGGCAT) in the general population?

IDS p.Ser69Ter (c.205_206insAAACTGGCAT) 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.Ser69Ter

c.205_206insAAACTGGCAT · rs2124065847 · VCV1065181

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

Consequence

nonsense (stop-gain)

predicted LoF

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.
Consequence	nonsense (stop-gain)	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 2 of 9
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 6.4	GERP 0.46, phastCons 1
Region caveats
Repeat context	seg dup	· reads may not map uniquely · confidence, not pathogenicity

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: IDS
Protein: p.Ser69Ter
Coding: c.205_206insAAACTGGCAT
MANE Select: NM_000202
dbSNP: rs2124065847
Type: Insertion
Location: chrX:149504191 (GRCh38)
Structure: AlphaFold pLDDT 93.39 · 2 PDB
Residue 69: an α-helix

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.Ser69= Likely benign ★ same residue
IDS p.Ser69Thr Likely benign ★ same residue
IDS c.240+2_240+3insTCCCAGA Likely pathogenic ★ same condition
IDS p.Ala30fs Pathogenic ★ same condition
IDS p.Ala414fs Pathogenic ★ same condition
IDS p.Asn38fs Likely pathogenic ★ same condition
IDS p.Asp147fs Pathogenic ★ same condition
IDS p.Asp320Ter 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-ser69ter (accessed [today's date]).

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