Is IDS p.Asp532Val (c.1595A>T) pathogenic?

IDS p.Asp532Val (c.1595A>T) is classified Uncertain significance in IDS (ClinVar, No assertion criteria, 1 submitter; last evaluated 2025-03-27). AlphaMissense: ambiguous (0.4918); Very rare (popmax 0.00651%, amr); Associated with mucopolysaccharidosis type 3A.

What condition is associated with IDS p.Asp532Val (c.1595A>T)?

IDS p.Asp532Val (c.1595A>T) is associated with mucopolysaccharidosis type 3A (ClinVar).

How common is IDS p.Asp532Val (c.1595A>T) in the general population?

IDS p.Asp532Val (c.1595A>T) is very rare (popmax 0.00651%, amr) (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.Asp532Val (c.1595A>T)?

AlphaMissense predicts ambiguous (score 0.4918) — an in-silico prediction, not a clinical call.

IDS p.Asp532Val

c.1595A>T · VCV4069638

Uncertain significance No assertion criteria

Classification

Uncertain significance

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4918 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00651%, amr)

Missense predictors

1/2 damaging

REVEL, SaProt · AlphaMissense indeterminate

Conditions

mucopolysaccharidosis type 3A

Computational evidence

Protein change
AlphaMissense	0.4918	ambiguous
REVEL	0.814	moderately pathogenic-leaning
SaProt	LLR -1.34	tolerated
⇒ REVEL calls this damaging; SaProt does not; AlphaMissense is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.9	GERP 0.62, phastCons 1
Regional constraint	o/e 0.78	unconstrained · MANE · 21 kb · p 5.6e-05 · regional, not allelic
Overall
CADD	24.9	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

Grpmax group 0.00651% Admixed American · 3/46,063 alleles

Filtering AF 0.00173% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000879%

Overall 0.000248% 3/1,212,011 alleles · very rare exomes 3/1,098,244 · genomes 0/113,767 · joint denominator

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.Asp532Val
Coding: c.1595A>T
MANE Select: NM_000202
Type: single nucleotide variant
Location: chrX:149482804 (GRCh38)
Structure: AlphaFold pLDDT 93.39 · 2 PDB

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.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
IDS p.Arg493Pro Pathogenic/Likely pathogenic ★★ same condition
IDS p.Pro480Leu Pathogenic/Likely pathogenic ★★ same condition
IDS p.Pro86Leu Pathogenic ★★ same condition
IDS p.Ala79Val 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-asp532val (accessed [today's date]).

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