Is IDUA p.Arg2= (c.6T>C) pathogenic?

IDUA p.Arg2= (c.6T>C) is classified Likely benign in IDUA (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-19). Very rare (popmax 0.00146%, afr); Associated with mucopolysaccharidosis type 1.

What condition is associated with IDUA p.Arg2= (c.6T>C)?

IDUA p.Arg2= (c.6T>C) is associated with mucopolysaccharidosis type 1 (ClinVar).

How common is IDUA p.Arg2= (c.6T>C) in the general population?

IDUA p.Arg2= (c.6T>C) is very rare (popmax 0.00146%, afr) (gnomAD).

How is Mucopolysaccharidosis type 1 inherited?

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

IDUA p.Arg2=

c.6T>C · rs918033021 · VCV2744372

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00146%, afr)

Conditions

mucopolysaccharidosis type 1

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.006	strongly benign-leaning
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -4.4	GERP -1.7
Overall
CADD	5.937	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00146% African / African-American · 1/68,336 alleles

Overall 6.77e-05% 1/1,476,856 alleles · very rare exomes 0/1,324,862 · genomes 1/151,994 · joint denominator

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: IDUA
Protein: p.Arg2=
Coding: c.6T>C
MANE Select: NM_000203
dbSNP: rs918033021
Type: single nucleotide variant
Location: chr4:987090 (GRCh38)

Full IDUA gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

mucopolysaccharidosis type 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Mucopolysaccharidosis type 1 (Orphanet):

Inheritance: Autosomal recessive
Onset: All ages
Prevalence: 1-9 / 100 000 (Europe)

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/idua-p-arg2 (accessed [today's date]).

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