Is IDS p.Asp275= (c.825C>T) pathogenic?

IDS p.Asp275= (c.825C>T) is classified Benign/Likely benign in IDS (ClinVar, Multiple submitters, 7 submitters; last evaluated 2026-01-24). Rare (popmax 0.233%, nfe); Associated with mucopolysaccharidosis type 2.

What condition is associated with IDS p.Asp275= (c.825C>T)?

IDS p.Asp275= (c.825C>T) is associated with mucopolysaccharidosis type 2, mucopolysaccharidosis type 3A (ClinVar).

How common is IDS p.Asp275= (c.825C>T) in the general population?

IDS p.Asp275= (c.825C>T) is rare (popmax 0.233%, nfe) (gnomAD).

How is Mucopolysaccharidosis type 2 inherited?

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

IDS p.Asp275=

c.825C>T · rs148038243 · VCV698195

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

gnomAD v4.1

Rare

rare (popmax 0.233%, nfe)

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 · no allele here is in the release
Constraint at this position
Conservation	phyloP -2.1	GERP -3.2
Overall
CADD	2.444	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.233% European (non-Finnish) · 2,081/894,510 alleles

Filtering AF 0.224% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.221%

Overall 0.18% 2,178/1,209,266 alleles · rare exomes 2,046/1,097,201 · genomes 132/112,065 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.233%	430
Remaining individualsnot grpmax-eligible	0.116%	865
Admixed American	0.0458%	2,182
Finnishnot grpmax-eligible	0.0193%	5,180
African / African-American	0.0157%	6,350
South Asian	0.00352%	28,415
East Asian	0.00296%	33,798

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.Asp275=
Coding: c.825C>T
MANE Select: NM_000202
dbSNP: rs148038243
Type: single nucleotide variant
Location: chrX:149496400 (GRCh38)
Structure: AlphaFold pLDDT 93.39 · 2 PDB
Residue 275: 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

Also linked: mucopolysaccharidosis type 3A

For Mucopolysaccharidosis type 2 (Orphanet):

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

Similar variants

IDS p.Asp275Asn Likely pathogenic ★★ same residue
IDS p.Asp275Tyr Likely pathogenic ★★ same residue
IDS p.Asp275Glu Uncertain significance ★ ⚠ 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
IDS c.1007-1G>A Pathogenic ★★ same condition
IDS c.1007-2A>C 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-asp275 (accessed [today's date]).

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