Is IDS p.Val89Ile (c.265G>A) pathogenic?

IDS p.Val89Ile (c.265G>A) is classified Uncertain significance in IDS (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-02). AlphaMissense: likely benign (0.1032); Very rare (popmax 0.00735%, amr); Associated with mucopolysaccharidosis type 2.

What condition is associated with IDS p.Val89Ile (c.265G>A)?

IDS p.Val89Ile (c.265G>A) is associated with mucopolysaccharidosis type 2 (ClinVar).

How common is IDS p.Val89Ile (c.265G>A) in the general population?

IDS p.Val89Ile (c.265G>A) is very rare (popmax 0.00735%, amr) (gnomAD).

How is Mucopolysaccharidosis type 2 inherited?

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

What do computational predictors say about IDS p.Val89Ile (c.265G>A)?

AlphaMissense predicts likely benign (score 0.1032) — an in-silico prediction, not a clinical call.

IDS p.Val89Ile

c.265G>A · VCV3705428

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1032 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00735%, amr)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Conditions

mucopolysaccharidosis type 2

Computational evidence

Protein change
AlphaMissense	0.1032	likely benign
REVEL	0.486	indeterminate
SaProt	LLR -8.71	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL is indeterminate.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 7.4	GERP 1.1, phastCons 1
Regional constraint	o/e 0.07	constrained · MANE · 819 bp · p 6.4e-10 · regional, not allelic
Overall
CADD	17.19	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00735% Admixed American · 3/40,826 alleles

Filtering AF 0.00195% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00104%

Overall 0.00138% 16/1,162,348 alleles · very rare exomes 16/1,049,475 · genomes 0/112,873 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00735%	13,609
European (non-Finnish)	0.00151%	66,250

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.Val89Ile
Coding: c.265G>A
MANE Select: NM_000202
Type: single nucleotide variant
Location: chrX:149503465 (GRCh38)
Structure: AlphaFold pLDDT 93.39 · 2 PDB
Residue 89: an α-helix; a UniProt-annotated variant site (in mps2)

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.Val89Phe Likely pathogenic ★ same residue
IDS p.Val89Gly Uncertain significance ★ ⚠ 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-val89ile (accessed [today's date]).

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