IDE p.Leu241=
c.723A>G · rs367823775 · VCV752005
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.116%, afr)
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 -0.59 | GERP -4.4, phastCons 0.035 |
| Overall | ||
| CADD | 4.201 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.116%
African / African-American · 87/74,866 alleles
Filtering AF
0.0965%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0892%
Overall
0.00577%
93/1,610,790 alleles · rare
exomes 43/1,458,582 · genomes 50/152,208 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.116% | 861 |
| Remaining individualsnot grpmax-eligible | 0.00481% | 20,795 |
| East Asian | 0.00223% | 44,814 |
| European (non-Finnish) | 0.00017% | 588,585 |
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
- IDE
- Protein
- p.Leu241=
- Coding
- c.723A>G
- MANE Select
- NM_004969
- dbSNP
- rs367823775
- Type
- single nucleotide variant
- Location
- chr10:92514981 (GRCh38)
- Gene constraint
- LOEUF 0.638 · pLI 0.08 (gnomAD)
- Structure
- AlphaFold pLDDT 94.06 · 62 PDB
- Residue 241
- an α-helix
Similar variants
- IDE p.Asn841= Benign ★★ same type
- IDE p.His10= Benign/Likely benign ★★ same type
- IDE p.Ile791= Benign ★★ same type
- IDE p.Ala185Glu Uncertain significance ★ ⚠ same type
- IDE p.Ala452Thr Uncertain significance ★ ⚠ same type
- IDE p.Ala479Thr Uncertain significance ★ ⚠ same type
- IDE p.Ala544Val Uncertain significance ★ ⚠ same type
- IDE p.Ala610Val Uncertain significance ★ ⚠ 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/ide-p-leu241 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown