Is IDUA p.Pro6= (c.18C>T) pathogenic?

IDUA p.Pro6= (c.18C>T) is classified Likely benign in IDUA (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-11). Very rare (popmax 0.00018%, nfe); Associated with mucopolysaccharidosis type 1.

What condition is associated with IDUA p.Pro6= (c.18C>T)?

IDUA p.Pro6= (c.18C>T) is associated with mucopolysaccharidosis type 1 (ClinVar).

How common is IDUA p.Pro6= (c.18C>T) in the general population?

IDUA p.Pro6= (c.18C>T) is very rare (popmax 0.00018%, nfe) (gnomAD).

How is Mucopolysaccharidosis type 1 inherited?

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

IDUA p.Pro6=

c.18C>T · rs1412821087 · VCV1648461

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00018%, nfe)

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	0.166	moderately benign-leaning
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -0.79	GERP -1.7
Overall
CADD	7.485	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00018% European (non-Finnish) · 2/1,110,302 alleles

Filtering AF 3e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.1e-05%

Overall 0.000137% 2/1,458,382 alleles · very rare exomes 2/1,306,242 · genomes 0/152,140 · 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.Pro6=
Coding: c.18C>T
MANE Select: NM_000203
dbSNP: rs1412821087
Type: single nucleotide variant
Location: chr4:987102 (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-pro6 (accessed [today's date]).

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