Is IDUA p.Arg313= (c.939G>A) pathogenic?

IDUA p.Arg313= (c.939G>A) is classified Likely benign in IDUA (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-11). Ultra-rare (popmax 0.0306%, eas); Associated with mucopolysaccharidosis type 1.

What condition is associated with IDUA p.Arg313= (c.939G>A)?

IDUA p.Arg313= (c.939G>A) is associated with mucopolysaccharidosis type 1 (ClinVar).

How common is IDUA p.Arg313= (c.939G>A) in the general population?

IDUA p.Arg313= (c.939G>A) is ultra-rare (popmax 0.0306%, eas) (gnomAD).

How is Mucopolysaccharidosis type 1 inherited?

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

IDUA p.Arg313=

c.939G>A · rs540430727 · VCV736913

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0306%, eas)

Conditions

mucopolysaccharidosis type 1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.187	benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.5	GERP -3.2, phastCons 1
Overall
CADD	7.008	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0306% East Asian · 13/42,462 alleles

Filtering AF 0.0181% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0143%

Overall 0.00115% 18/1,566,212 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0306%	3,266
Remaining individualsnot grpmax-eligible	0.00494%	20,240
South Asian	0.00117%	85,402
European (non-Finnish)	8.65e-05%	1,156,128

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.Arg313=
Coding: c.939G>A
MANE Select: NM_000203
dbSNP: rs540430727
Type: single nucleotide variant
Location: chr4:1002128 (GRCh38)
Gene constraint: LOEUF 1.344 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 95.12 · 11 PDB
Residue 313: an α-helix

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)

Similar variants

SLC26A1 p.Lys313Glu Likely benign ★ same residue
IDUA c.1190-10C>A Likely pathogenic ★★★ same condition
IDUA c.1190-1G>A Pathogenic ★★★ same condition
IDUA c.1402+1G>A Likely pathogenic ★★★ same condition
IDUA c.1402+1G>T Likely pathogenic ★★★ same condition
IDUA c.1402+2T>G Likely pathogenic ★★★ same condition
IDUA c.1403-1G>T Pathogenic ★★★ same condition
IDUA c.1650+1G>T 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/idua-p-arg313 (accessed [today's date]).

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