Is IDS p.His112= (c.336C>T) pathogenic?

IDS p.His112= (c.336C>T) is classified Benign/Likely benign in IDS (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-01-24). Rare (popmax 0.236%, afr); Associated with Inborn genetic diseases.

What condition is associated with IDS p.His112= (c.336C>T)?

IDS p.His112= (c.336C>T) is associated with Inborn genetic diseases, mucopolysaccharidosis type 3A, mucopolysaccharidosis type 2 (ClinVar).

How common is IDS p.His112= (c.336C>T) in the general population?

IDS p.His112= (c.336C>T) is rare (popmax 0.236%, afr) (gnomAD).

IDS p.His112=

c.336C>T · rs138687038 · VCV791680

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

rare (popmax 0.236%, afr)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1	GERP -2.2
Overall
CADD	0.632	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.236% African / African-American · 133/56,386 alleles

Filtering AF 0.203% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.191%

Overall 0.019% 227/1,192,970 alleles · rare exomes 152/1,082,167 · genomes 75/110,803 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.236%	424
Admixed American	0.0208%	4,809
Remaining individualsnot grpmax-eligible	0.0128%	7,831
European (non-Finnish)	0.0088%	11,362
South Asian	0.00183%	54,676

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.His112=
Coding: c.336C>T
MANE Select: NM_000202
dbSNP: rs138687038
Type: single nucleotide variant
Location: chrX:149503394 (GRCh38)
Structure: AlphaFold pLDDT 93.39 · 2 PDB
Residue 112: an α-helix

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

Similar variants

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
IDS c.103+1G>A Pathogenic ★★ same condition
IDS c.104-2A>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-his112 (accessed [today's date]).

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