Is IDUA p.Val97= (c.291C>T) pathogenic?

IDUA p.Val97= (c.291C>T) is classified Likely benign in IDUA (ClinVar, Single submitter, 1 submitter; last evaluated 2026-01-28). Very rare (popmax 0.00232%, eas); Associated with mucopolysaccharidosis type 1.

What condition is associated with IDUA p.Val97= (c.291C>T)?

IDUA p.Val97= (c.291C>T) is associated with mucopolysaccharidosis type 1 (ClinVar).

How common is IDUA p.Val97= (c.291C>T) in the general population?

IDUA p.Val97= (c.291C>T) is very rare (popmax 0.00232%, eas) (gnomAD).

How is Mucopolysaccharidosis type 1 inherited?

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

IDUA p.Val97=

c.291C>T · rs1713872837 · VCV2967972

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00232%, eas)

Conditions

mucopolysaccharidosis type 1

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 0.36	GERP 0.64, phastCons 0.99
Overall
CADD	13.46	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00232% East Asian · 1/43,146 alleles

Overall 0.000189% 3/1,584,268 alleles · very rare exomes 2/1,431,914 · genomes 1/152,354 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00232%	43,146
Admixed American	0.00179%	55,908
European (non-Finnish)	8.58e-05%	1,165,589

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.Val97=
Coding: c.291C>T
MANE Select: NM_000203
dbSNP: rs1713872837
Type: single nucleotide variant
Location: chr4:987941 (GRCh38)
Gene constraint: LOEUF 1.344 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 95.12 · 11 PDB

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

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
IDUA c.1650+5G>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/idua-p-val97 (accessed [today's date]).

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