Is IDS p.Gly9= (c.27C>T) pathogenic?

IDS p.Gly9= (c.27C>T) is classified Benign in IDS (ClinVar, Single submitter, 1 submitter; last evaluated 2026-01-14). Ultra-rare (popmax 0.0499%, sas); Associated with mucopolysaccharidosis type 2.

What condition is associated with IDS p.Gly9= (c.27C>T)?

IDS p.Gly9= (c.27C>T) is associated with mucopolysaccharidosis type 2 (ClinVar).

How common is IDS p.Gly9= (c.27C>T) in the general population?

IDS p.Gly9= (c.27C>T) is ultra-rare (popmax 0.0499%, 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.Gly9=

c.27C>T · rs782412902 · VCV1166583

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0499%, sas)

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 0.64	GERP 0.24, phastCons 0.69
Overall
CADD	6.174	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0499% South Asian · 28/56,146 alleles

Filtering AF 0.0353% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0305%

Overall 0.00267% 32/1,197,626 alleles · ultra-rare exomes 32/1,085,919 · genomes 0/111,707 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0499%	2,005
Remaining individualsnot grpmax-eligible	0.00639%	15,648
European (non-Finnish)	0.000113%	885,779

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.Gly9=
Coding: c.27C>T
MANE Select: NM_000202
dbSNP: rs782412902
Type: single nucleotide variant
Location: chrX:149505111 (GRCh38)
Structure: AlphaFold pLDDT 93.39 · 2 PDB

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 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
IDS c.1007-8T>G Pathogenic/Likely pathogenic ★★ same condition
IDS c.103+1G>A Pathogenic ★★ same condition
IDS c.104-2A>G 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-gly9 (accessed [today's date]).

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