Is IDS p.Pro358= (c.1074C>G) pathogenic?

IDS p.Pro358= (c.1074C>G) is classified Benign/Likely benign in IDS (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-01-30). Ultra-rare (popmax 0.0581%, sas); Associated with Inborn genetic diseases.

What condition is associated with IDS p.Pro358= (c.1074C>G)?

IDS p.Pro358= (c.1074C>G) is associated with Inborn genetic diseases, mucopolysaccharidosis type 2 (ClinVar).

How common is IDS p.Pro358= (c.1074C>G) in the general population?

IDS p.Pro358= (c.1074C>G) is ultra-rare (popmax 0.0581%, sas) (gnomAD).

IDS p.Pro358=

c.1074C>G · rs61736891 · VCV590213

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0581%, sas)

Conditions

Inborn genetic diseases

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -0.2	GERP -2.5, phastCons 0.03
Overall
CADD	1.155	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0581% South Asian · 33/56,806 alleles

Filtering AF 0.0535% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0519%

Overall 0.0579% 701/1,209,739 alleles · ultra-rare exomes 663/1,097,776 · genomes 38/111,963 · joint denominator

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.217%	462
Remaining individualsnot grpmax-eligible	0.0924%	1,082
South Asiangrpmax	0.0581%	1,721
European (non-Finnish)	0.0577%	1,734
Middle Eastern	0.046%	2,174
African / African-American	0.00525%	19,061
Admixed American	0.00436%	22,920

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Pro358=
Coding: c.1074C>G
MANE Select: NM_000202
dbSNP: rs61736891
Type: single nucleotide variant
Location: chrX:149487031 (GRCh38)

Full IDS gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: mucopolysaccharidosis type 2

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-pro358 (accessed [today's date]).

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