Is IDS p.Thr93= (c.279T>A) pathogenic?

IDS p.Thr93= (c.279T>A) is classified Uncertain significance in IDS (ClinVar, Single submitter, 1 submitter; last evaluated 2022-02-28). Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with IDS p.Thr93= (c.279T>A)?

IDS p.Thr93= (c.279T>A) is associated with Inborn genetic diseases (ClinVar).

How common is IDS p.Thr93= (c.279T>A) in the general population?

IDS p.Thr93= (c.279T>A) is absent from gnomAD v4.1 (gnomAD).

IDS p.Thr93=

c.279T>A · rs2520896919 · VCV2397856

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.92	acceptor gain · deltas
Pangolin	Δ0.76	gain · loss 0.38 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP -5.4	GERP -2.2
Overall
CADD	18.38	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: IDS
Protein: p.Thr93=
Coding: c.279T>A
MANE Select: NM_000202
dbSNP: rs2520896919
Type: single nucleotide variant
Location: chrX:149503451 (GRCh38)
Structure: AlphaFold pLDDT 93.39 · 2 PDB
Residue 93: 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

Similar variants

IDS p.Arg172Ter Pathogenic ★★ same condition
IDS p.Asp269Val Pathogenic/Likely pathogenic ★★ same condition
IDS p.Pro469Arg Likely pathogenic ★★ same condition
IDS p.Ser71Arg Likely pathogenic ★★ same condition
IDS p.Tyr499Ter Pathogenic/Likely pathogenic ★★ same condition
IDS p.Ala317Asp Uncertain significance ★★ ⚠ same condition
IDS p.Arg101His Uncertain significance ★★ ⚠ same condition
IDS p.Arg445Ser Uncertain significance ★★ ⚠ 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-thr93 (accessed [today's date]).

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