Is IDS p.Arg5Trp (c.13C>T) pathogenic?

IDS p.Arg5Trp (c.13C>T) is classified Benign in IDS (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-22). AlphaMissense: likely benign (0.1019); Ultra-rare (popmax 0.0161%, sas); Associated with mucopolysaccharidosis type 2.

What condition is associated with IDS p.Arg5Trp (c.13C>T)?

IDS p.Arg5Trp (c.13C>T) is associated with mucopolysaccharidosis type 2 (ClinVar).

How common is IDS p.Arg5Trp (c.13C>T) in the general population?

IDS p.Arg5Trp (c.13C>T) is ultra-rare (popmax 0.0161%, sas) (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.Arg5Trp (c.13C>T)?

AlphaMissense predicts likely benign (score 0.1019) — an in-silico prediction, not a clinical call.

IDS p.Arg5Trp

c.13C>T · rs141900718 · VCV1550671

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1019 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0161%, sas)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

mucopolysaccharidosis type 2

Computational evidence

Protein change
AlphaMissense	0.1019	likely benign
REVEL	0.458	indeterminate
SaProt	LLR -7.44	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.41	GERP -1.3, phastCons 0.001
Regional constraint	o/e 1.34	unconstrained · MANE · 858 bp · p 0.049 · regional, not allelic
Overall
CADD	9.007	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 0.0161% South Asian · 9/55,870 alleles

Filtering AF 0.00835% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00626%

Overall 0.00109% 13/1,192,020 alleles · ultra-rare exomes 12/1,080,236 · genomes 1/111,784 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0161%	6,208
Ashkenazi Jewishnot grpmax-eligible	0.00461%	21,700
East Asian	0.00302%	33,091
African / African-American	0.00177%	56,625
European (non-Finnish)	0.000113%	881,345

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.Arg5Trp
Coding: c.13C>T
MANE Select: NM_000202
dbSNP: rs141900718
Type: single nucleotide variant
Location: chrX:149505125 (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.Arg5= Likely benign ★ same residue
IDS p.Arg5fs Pathogenic ★ 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

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-arg5trp (accessed [today's date]).

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