Is IDS p.Val283= (c.849G>C) pathogenic?

IDS p.Val283= (c.849G>C) is classified Benign/Likely benign in IDS (ClinVar, Multiple submitters, 5 submitters; last evaluated 2025-11-18). Ultra-rare (popmax 0.0185%, nfe); Associated with mucopolysaccharidosis type 2.

What condition is associated with IDS p.Val283= (c.849G>C)?

IDS p.Val283= (c.849G>C) is associated with mucopolysaccharidosis type 2, mucopolysaccharidosis type 3A (ClinVar).

How common is IDS p.Val283= (c.849G>C) in the general population?

IDS p.Val283= (c.849G>C) is ultra-rare (popmax 0.0185%, nfe) (gnomAD).

How is Mucopolysaccharidosis type 2 inherited?

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

IDS p.Val283=

c.849G>C · rs147374356 · VCV733577

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0185%, nfe)

Conditions

mucopolysaccharidosis type 2

⚠ 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 -0.19	GERP -1.8, phastCons 0.2
Overall
CADD	4.542	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0185% European (non-Finnish) · 166/895,096 alleles

Filtering AF 0.0162% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0154%

Overall 0.0141% 171/1,210,009 alleles · ultra-rare exomes 149/1,097,805 · genomes 22/112,204 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0185%	5,392
Finnishnot grpmax-eligible	0.00643%	15,561
Remaining individualsnot grpmax-eligible	0.0042%	23,786

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.Val283=
Coding: c.849G>C
MANE Select: NM_000202
dbSNP: rs147374356
Type: single nucleotide variant
Location: chrX:149496376 (GRCh38)

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

Also linked: mucopolysaccharidosis type 3A

For Mucopolysaccharidosis type 2 (Orphanet):

Inheritance: X-linked recessive
Onset: Childhood
Prevalence: 1-9 / 1 000 000 (Europe)

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-val283 (accessed [today's date]).

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