Is IDS p.Lys295Arg (c.884A>G) pathogenic?

IDS p.Lys295Arg (c.884A>G) is classified Benign/Likely benign in IDS (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-24). AlphaMissense: likely benign (0.0818); Rare (popmax 0.244%, afr); Associated with Inborn genetic diseases.

What condition is associated with IDS p.Lys295Arg (c.884A>G)?

IDS p.Lys295Arg (c.884A>G) is associated with Inborn genetic diseases, mucopolysaccharidosis type 3A, mucopolysaccharidosis type 2 (ClinVar).

How common is IDS p.Lys295Arg (c.884A>G) in the general population?

IDS p.Lys295Arg (c.884A>G) is rare (popmax 0.244%, afr) (gnomAD).

What do computational predictors say about IDS p.Lys295Arg (c.884A>G)?

AlphaMissense predicts likely benign (score 0.0818) — an in-silico prediction, not a clinical call.

IDS p.Lys295Arg

c.884A>G · rs113993953 · VCV791679

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.0818 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.244%, afr)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

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
AlphaMissense	0.0818	likely benign
REVEL	0.358	indeterminate
SaProt	LLR -5.40	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL is indeterminate.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 4.2	GERP 1.6, phastCons 1
Regional constraint	o/e 0.78	unconstrained · MANE · 21 kb · p 5.6e-05 · regional, not allelic
Overall
CADD	16.63	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 0.244% African / African-American · 139/57,008 alleles

Filtering AF 0.211% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.198%

Overall 0.0132% 160/1,209,378 alleles · rare exomes 86/1,097,752 · genomes 74/111,626 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.244%	410
Middle Eastern	0.0229%	4,374
Admixed American	0.0197%	5,082
Remaining individualsnot grpmax-eligible	0.0168%	5,948
South Asian	0.00352%	28,409
European (non-Finnish)	0.000112%	894,879

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.Lys295Arg
Coding: c.884A>G
MANE Select: NM_000202
dbSNP: rs113993953
Type: single nucleotide variant
Location: chrX:149490436 (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 3A 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-lys295arg (accessed [today's date]).

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