Is IDS p.Pro86= (c.258G>A) pathogenic?

IDS p.Pro86= (c.258G>A) is classified Likely benign in IDS (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-23). Very rare (popmax 0.00181%, afr); Associated with mucopolysaccharidosis type 2.

What condition is associated with IDS p.Pro86= (c.258G>A)?

IDS p.Pro86= (c.258G>A) is associated with mucopolysaccharidosis type 2 (ClinVar).

How common is IDS p.Pro86= (c.258G>A) in the general population?

IDS p.Pro86= (c.258G>A) is very rare (popmax 0.00181%, afr) (gnomAD).

How is Mucopolysaccharidosis type 2 inherited?

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

IDS p.Pro86=

c.258G>A · rs1557340277 · VCV3009382

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00181%, afr)

Conditions

mucopolysaccharidosis type 2

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.40	acceptor gain · deltas
Pangolin	Δ0.24	gain · loss 0.10 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP -6.7	GERP -2.2
Overall
CADD	14.64	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00181% African / African-American · 1/55,276 alleles

Filtering AF 9.4e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.6e-05%

Overall 0.00035% 4/1,142,041 alleles · very rare exomes 3/1,031,572 · genomes 1/110,469 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00181%	55,276
European (non-Finnish)	0.000355%	281,933

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.Pro86=
Coding: c.258G>A
MANE Select: NM_000202
dbSNP: rs1557340277
Type: single nucleotide variant
Location: chrX:149503472 (GRCh38)
Structure: AlphaFold pLDDT 93.39 · 2 PDB
Residue 86: an α-helix; a UniProt-annotated variant site (in mps2; intermediate to severe forms); a UniProt-annotated variant site (in mps2); a UniProt-annotated variant site (in mps2; severe form)

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.Pro86Arg Pathogenic ★★ same residue
IDS p.Pro86Leu Pathogenic ★★ same residue
IDS p.Pro86Gln Pathogenic ★ same residue
IDS p.Pro86fs 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

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-pro86 (accessed [today's date]).

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