Is IDS p.Asp35Tyr (c.103G>T) pathogenic?

IDS p.Asp35Tyr (c.103G>T) is classified Likely pathogenic in IDS (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-26). AlphaMissense: likely benign (0.0984); No allele count reported in gnomAD v4.1 (AN 1,201,988); Associated with Inborn genetic diseases.

What condition is associated with IDS p.Asp35Tyr (c.103G>T)?

IDS p.Asp35Tyr (c.103G>T) is associated with Inborn genetic diseases (ClinVar).

How common is IDS p.Asp35Tyr (c.103G>T) in the general population?

IDS p.Asp35Tyr (c.103G>T) is no allele count reported in gnomAD v4.1 (AN 1,201,988) (gnomAD).

What do computational predictors say about IDS p.Asp35Tyr (c.103G>T)?

AlphaMissense predicts likely benign (score 0.0984) — an in-silico prediction, not a clinical call.

IDS p.Asp35Tyr

c.103G>T · VCV3859389

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0984 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,201,988)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0984	likely benign ⚠ discordant with ClinVar
REVEL	0.464	indeterminate
SaProt	LLR -6.93	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	Δ0.73	donor loss · deltas
Pangolin	Δ0.77	loss · gain 0.02 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 6.6	GERP 1.3, phastCons 1
Regional constraint	o/e 1.34	unconstrained · MANE · 858 bp · p 0.049 · regional, not allelic
Overall
CADD	26.8	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

No allele count reported in gnomAD v4.1 (AN 1,201,988). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: IDS
Protein: p.Asp35Tyr
Coding: c.103G>T
MANE Select: NM_000202
Type: single nucleotide variant
Location: chrX:149505035 (GRCh38)
Structure: AlphaFold pLDDT 93.39 · 2 PDB

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.Asp35His Likely pathogenic ★★ ⚠ same residue
IDS p.Asp35Gly Conflicting classifications of pathogenicity ★ ⚠ same residue
IDS p.Asp35Val Uncertain significance ★ ⚠ same residue
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

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-asp35tyr (accessed [today's date]).

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