Is IDS p.Tyr306= (c.918T>C) pathogenic?

IDS p.Tyr306= (c.918T>C) is classified Likely benign in IDS (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-12). Ultra-rare (popmax 0.0118%, eas); Associated with mucopolysaccharidosis type 2.

What condition is associated with IDS p.Tyr306= (c.918T>C)?

IDS p.Tyr306= (c.918T>C) is associated with mucopolysaccharidosis type 2 (ClinVar).

How common is IDS p.Tyr306= (c.918T>C) in the general population?

IDS p.Tyr306= (c.918T>C) is ultra-rare (popmax 0.0118%, eas) (gnomAD).

How is Mucopolysaccharidosis type 2 inherited?

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

IDS p.Tyr306=

c.918T>C · rs781920980 · VCV1116167

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0118%, eas)

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 0.48	GERP -2.5, phastCons 0.002
Overall
CADD	1.907	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0118% East Asian · 4/33,844 alleles

Filtering AF 0.00395% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00235%

Overall 0.000413% 5/1,210,588 alleles · ultra-rare exomes 5/1,096,741 · genomes 0/113,847 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0118%	8,461
European (non-Finnish)	0.000112%	894,230

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.Tyr306=
Coding: c.918T>C
MANE Select: NM_000202
dbSNP: rs781920980
Type: single nucleotide variant
Location: chrX:149490402 (GRCh38)
Structure: AlphaFold pLDDT 93.39 · 2 PDB
Residue 306: 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.Tyr306His 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
IDS c.1007-8T>G Pathogenic/Likely pathogenic ★★ same condition
IDS c.103+1G>A 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-tyr306 (accessed [today's date]).

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