Is IDS p.Arg95= (c.285G>A) pathogenic?

IDS p.Arg95= (c.285G>A) is classified Likely benign in IDS (ClinVar, Single submitter, 1 submitter; last evaluated 2023-02-23). Very rare (popmax 0.00184%, sas); Associated with mucopolysaccharidosis type 2.

What condition is associated with IDS p.Arg95= (c.285G>A)?

IDS p.Arg95= (c.285G>A) is associated with mucopolysaccharidosis type 2 (ClinVar).

How common is IDS p.Arg95= (c.285G>A) in the general population?

IDS p.Arg95= (c.285G>A) is very rare (popmax 0.00184%, sas) (gnomAD).

How is Mucopolysaccharidosis type 2 inherited?

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

IDS p.Arg95=

c.285G>A · rs782779732 · VCV1148083

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00184%, sas)

Conditions

mucopolysaccharidosis type 2

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.32	acceptor loss · deltas
Constraint at this position
Conservation	phyloP 2.1	GERP 0.076, phastCons 1
Overall
CADD	12.92	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00184% South Asian · 1/54,453 alleles

Filtering AF 0.000167% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000122%

Overall 0.000508% 6/1,180,172 alleles · very rare exomes 6/1,067,125 · genomes 0/113,047 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00184%	54,453
European (non-Finnish)	0.000571%	175,116

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: IDS
Protein: p.Arg95=
Coding: c.285G>A
MANE Select: NM_000202
dbSNP: rs782779732
Type: single nucleotide variant
Location: chrX:149503445 (GRCh38)
Structure: AlphaFold pLDDT 93.39 · 2 PDB
Residue 95: a UniProt-annotated variant site (in mps2; intermediate form); a UniProt-annotated variant site (in mps2; mild form); a UniProt-annotated variant site (in mps2; severe form)

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.Arg95Gly Pathogenic/Likely pathogenic ★★ same residue
IDS p.Arg95Ser Pathogenic ★ same residue
IDS p.Arg95Thr Pathogenic ★ same residue
IDS p.Arg95Trp Pathogenic ★ same residue
IDS p.Arg95fs Pathogenic ★ same residue
IDS c.1006+1G>C Pathogenic ★★ same condition
IDS c.1006+1G>T Pathogenic ★★ same condition
IDS c.1007-133A>G 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-arg95 (accessed [today's date]).

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