IDS p.Leu548Ter
c.1643T>A · rs2520751814 · VCV2506151
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | escapes | premature termination codon in the last exon (9 of 9) — the truncated protein is likely expressed. PVS1 input, not an applied code |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 2 | GERP -1.3, phastCons 0.001 |
| Overall | ||
| CADD | 29.7 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
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.Leu548Ter
- Coding
- c.1643T>A
- MANE Select
- NM_000202
- dbSNP
- rs2520751814
- Type
- single nucleotide variant
- Location
- chrX:149482756 (GRCh38)
- Structure
- AlphaFold pLDDT 93.39 · 2 PDB
- Residue 548
- an α-helix
Similar variants
- IDS p.Leu548Phe Uncertain significance ★ ⚠ same residue
- IDS p.Leu548= Likely benign ★ same residue
- IDS c.1006+1G>C Pathogenic ★★ same type
- IDS c.1006+1G>T Pathogenic ★★ same type
- IDS c.1007-133A>G Likely pathogenic ★★ same type
- IDS c.1007-1G>A Pathogenic ★★ same type
- IDS c.1007-2A>C Pathogenic/Likely pathogenic ★★ same type
- IDS c.1007-8T>G Pathogenic/Likely pathogenic ★★ same type
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-leu548ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown