Is IDS p.Arg458His (c.1373G>A) pathogenic?

IDS p.Arg458His (c.1373G>A) is classified Conflicting classifications of pathogenicity in IDS (ClinVar, Conflicting submitters, 3 submitters; last evaluated 2025-01-13). AlphaMissense: likely benign (0.0823); Ultra-rare (popmax 0.0119%, eas); Associated with mucopolysaccharidosis type 2.

What condition is associated with IDS p.Arg458His (c.1373G>A)?

IDS p.Arg458His (c.1373G>A) is associated with mucopolysaccharidosis type 2 (ClinVar).

How common is IDS p.Arg458His (c.1373G>A) in the general population?

IDS p.Arg458His (c.1373G>A) is ultra-rare (popmax 0.0119%, eas) (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.Arg458His (c.1373G>A)?

AlphaMissense predicts likely benign (score 0.0823) — an in-silico prediction, not a clinical call.

IDS p.Arg458His

c.1373G>A · rs782697859 · VCV2148543

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.0823 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0119%, eas)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Conditions

mucopolysaccharidosis type 2

Computational evidence

Protein change
AlphaMissense	0.0823	likely benign
REVEL	0.399	indeterminate
SaProt	LLR -6.35	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.42	GERP -0.53, phastCons 0.047
Regional constraint	o/e 0.78	unconstrained · MANE · 21 kb · p 5.6e-05 · regional, not allelic
Overall
CADD	18.26	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 0.0119% East Asian · 4/33,706 alleles

Filtering AF 0.00396% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00236%

Overall 0.00166% 20/1,207,030 alleles · ultra-rare exomes 17/1,095,384 · genomes 3/111,646 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0119%	8,427
Remaining individualsnot grpmax-eligible	0.00632%	15,824
African / African-American	0.00526%	19,016
South Asian	0.00353%	28,354
European (non-Finnish)	0.000896%	111,613

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.Arg458His
Coding: c.1373G>A
MANE Select: NM_000202
dbSNP: rs782697859
Type: single nucleotide variant
Location: chrX:149483026 (GRCh38)
Structure: AlphaFold pLDDT 93.39 · 2 PDB
Residue 458: an α-helix

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.Arg458Cys Conflicting classifications of pathogenicity ★ ⚠ 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
IDS c.103+1G>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/ids-p-arg458his (accessed [today's date]).

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