Is IDS p.Tyr103= (c.309C>T) pathogenic?

IDS p.Tyr103= (c.309C>T) is classified Likely benign in IDS (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-05-18). Very rare (popmax 0.00951%, amr); Associated with mucopolysaccharidosis type 2.

What condition is associated with IDS p.Tyr103= (c.309C>T)?

IDS p.Tyr103= (c.309C>T) is associated with mucopolysaccharidosis type 2 (ClinVar).

How common is IDS p.Tyr103= (c.309C>T) in the general population?

IDS p.Tyr103= (c.309C>T) is very rare (popmax 0.00951%, amr) (gnomAD).

How is Mucopolysaccharidosis type 2 inherited?

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

IDS p.Tyr103=

c.309C>T · rs1174495581 · VCV1085105

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00951%, amr)

Conditions

mucopolysaccharidosis type 2

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 2.8	GERP 0.015, phastCons 1
Overall
CADD	6.455	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00951% Admixed American · 4/42,073 alleles

Filtering AF 0.00322% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00189%

Overall 0.00076% 9/1,183,597 alleles · very rare exomes 6/1,072,806 · genomes 3/110,791 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00951%	10,518
Remaining individualsnot grpmax-eligible	0.00429%	23,324
South Asian	0.00184%	54,318
European (non-Finnish)	0.000227%	439,789

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.Tyr103=
Coding: c.309C>T
MANE Select: NM_000202
dbSNP: rs1174495581
Type: single nucleotide variant
Location: chrX:149503421 (GRCh38)
Structure: AlphaFold pLDDT 93.39 · 2 PDB
Residue 103: a β-strand

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.Tyr103Ter Pathogenic ★★ same residue
IDS p.Tyr103Asp Likely 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
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

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-tyr103 (accessed [today's date]).

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