Is IDS p.Pro469Ser (c.1405C>T) pathogenic?

IDS p.Pro469Ser (c.1405C>T) is classified Uncertain significance in IDS (ClinVar, No assertion criteria, 1 submitter; last evaluated 2025-05-08). AlphaMissense: likely pathogenic (0.7416); Absent from gnomAD v4.1; Associated with mucopolysaccharidosis type 3A.

What condition is associated with IDS p.Pro469Ser (c.1405C>T)?

IDS p.Pro469Ser (c.1405C>T) is associated with mucopolysaccharidosis type 3A (ClinVar).

How common is IDS p.Pro469Ser (c.1405C>T) in the general population?

IDS p.Pro469Ser (c.1405C>T) is absent from gnomAD v4.1 (gnomAD).

How is Mucopolysaccharidosis type 3 inherited?

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

What do computational predictors say about IDS p.Pro469Ser (c.1405C>T)?

AlphaMissense predicts likely pathogenic (score 0.7416) — an in-silico prediction, not a clinical call.

IDS p.Pro469Ser

c.1405C>T · VCV4069630

Uncertain significance No assertion criteria

Classification

Uncertain significance

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.7416 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

mucopolysaccharidosis type 3A

Computational evidence

Protein change
AlphaMissense	0.7416	likely pathogenic
REVEL	0.828	moderately pathogenic-leaning
SaProt	LLR -9.83	tolerated
⇒ AlphaMissense and REVEL call this damaging; SaProt does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.6, phastCons 1
Regional constraint	o/e 0.78	unconstrained · MANE · 21 kb · p 5.6e-05 · regional, not allelic
Overall
CADD	24.0	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.Pro469Ser
Coding: c.1405C>T
MANE Select: NM_000202
Type: single nucleotide variant
Location: chrX:149482994 (GRCh38)
Structure: AlphaFold pLDDT 93.39 · 2 PDB
Residue 469: a UniProt-annotated variant site (in mps2; mild form); a β-strand

Full IDS gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

mucopolysaccharidosis type 3A — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Mucopolysaccharidosis type 3 (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood
Prevalence: 1-9 / 1 000 000 (Brazil)

Similar variants

IDS p.Pro469Arg Likely pathogenic ★★ same residue
IDS p.Pro469Leu Likely pathogenic ★★ same residue
IDS p.Pro469Ala Uncertain significance ★★ ⚠ same residue
IDS p.Pro469His Likely pathogenic ★ same residue
IDS p.Ala346Val Pathogenic/Likely pathogenic ★★ ⚠ same condition
IDS p.Ala85Asp Pathogenic/Likely pathogenic ★★ same condition
IDS p.Arg443Ter Pathogenic ★★ same condition
IDS p.Arg468Trp 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-pro469ser (accessed [today's date]).

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