Is IDS p.Val89Gly (c.266T>G) pathogenic?

IDS p.Val89Gly (c.266T>G) is classified Uncertain significance in IDS (ClinVar, Single submitter, 1 submitter; last evaluated 2021-09-20). AlphaMissense: ambiguous (0.5149); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with IDS p.Val89Gly (c.266T>G)?

IDS p.Val89Gly (c.266T>G) is associated with Inborn genetic diseases (ClinVar).

How common is IDS p.Val89Gly (c.266T>G) in the general population?

IDS p.Val89Gly (c.266T>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about IDS p.Val89Gly (c.266T>G)?

AlphaMissense predicts ambiguous (score 0.5149) — an in-silico prediction, not a clinical call.

IDS p.Val89Gly

c.266T>G · rs2520896995 · VCV1794541

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.5149 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

REVEL, SaProt · AlphaMissense indeterminate

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.5149	ambiguous
REVEL	0.827	moderately pathogenic-leaning
SaProt	LLR -11.57	damaging
⇒ REVEL and SaProt both call this damaging; AlphaMissense is indeterminate.
Splicing
SpliceAI	Δ0.26	acceptor loss · deltas
Constraint at this position
Conservation	phyloP 11	GERP 1.1, phastCons 1
Regional constraint	o/e 0.07	constrained · MANE · 819 bp · p 6.4e-10 · regional, not allelic
Overall
CADD	23.2	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: IDS
Protein: p.Val89Gly
Coding: c.266T>G
MANE Select: NM_000202
dbSNP: rs2520896995
Type: single nucleotide variant
Location: chrX:149503464 (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

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

IDS p.Val89Phe Likely pathogenic ★ same residue
IDS p.Val89Ile Uncertain significance ★ ⚠ same residue
IDS p.Arg172Ter Pathogenic ★★ same condition
IDS p.Asp269Val Pathogenic/Likely pathogenic ★★ same condition
IDS p.Pro469Arg Likely pathogenic ★★ same condition
IDS p.Ser71Arg Likely pathogenic ★★ same condition
IDS p.Tyr499Ter Pathogenic/Likely pathogenic ★★ same condition
IDS p.Ala317Asp Uncertain significance ★★ ⚠ 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-val89gly (accessed [today's date]).

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