Is IDS p.Arg445His (c.1334G>A) pathogenic?

IDS p.Arg445His (c.1334G>A) is classified Conflicting classifications of pathogenicity in IDS (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2025-11-12). AlphaMissense: likely benign (0.0582); Very rare (popmax 0.00891%, eas); Associated with mucopolysaccharidosis type 2.

What condition is associated with IDS p.Arg445His (c.1334G>A)?

IDS p.Arg445His (c.1334G>A) is associated with mucopolysaccharidosis type 2 (ClinVar).

How common is IDS p.Arg445His (c.1334G>A) in the general population?

IDS p.Arg445His (c.1334G>A) is very rare (popmax 0.00891%, 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.Arg445His (c.1334G>A)?

AlphaMissense predicts likely benign (score 0.0582) — an in-silico prediction, not a clinical call.

IDS p.Arg445His

c.1334G>A · rs782371096 · VCV2140647

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0582 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00891%, eas)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Conditions

mucopolysaccharidosis type 2

Computational evidence

Protein change
AlphaMissense	0.0582	likely benign
REVEL	0.321	indeterminate
SaProt	LLR -6.49	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 -3.2	GERP -3.2
Regional constraint	o/e 0.78	unconstrained · MANE · 21 kb · p 5.6e-05 · regional, not allelic
Overall
CADD	0.044	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 0.00891% East Asian · 3/33,661 alleles

Filtering AF 0.00236% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00125%

Overall 0.00158% 19/1,205,011 alleles · very rare exomes 16/1,093,450 · genomes 3/111,561 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00891%	11,220
South Asian	0.00532%	18,807
Remaining individualsnot grpmax-eligible	0.00211%	47,406
African / African-American	0.00175%	57,000
European (non-Finnish)	0.00123%	81,061

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.Arg445His
Coding: c.1334G>A
MANE Select: NM_000202
dbSNP: rs782371096
Type: single nucleotide variant
Location: chrX:149483065 (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 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.Arg445= Likely benign ★ same residue
IDS p.Arg445Cys Likely benign ★ same residue
IDS p.Arg445Ser 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

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-arg445his (accessed [today's date]).

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