IDE p.His10=
c.30C>T · rs554481643 · VCV788067
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.753%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.64 | GERP -4, phastCons 0.86 |
| Overall | ||
| CADD | 7.407 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.753%
Middle Eastern · 43/5,708 alleles
Filtering AF
0.575%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.512%
Overall
0.0649%
981/1,511,746 alleles · rare
exomes 870/1,359,386 · genomes 111/152,360 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.753% | 133 |
| South Asian | 0.384% | 260 |
| African / African-American | 0.148% | 675 |
| Remaining individualsnot grpmax-eligible | 0.126% | 793 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0836% | 1,196 |
| Admixed American | 0.0573% | 1,746 |
| European (non-Finnish) | 0.0344% | 2,903 |
| Finnishnot grpmax-eligible | 0.0216% | 4,623 |
| East Asian | 0.00823% | 12,158 |
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.His10=
- Coding
- c.30C>T
- MANE Select
- NM_004969
- dbSNP
- rs554481643
- Type
- single nucleotide variant
- Location
- chr10:92573990 (GRCh38)
- Gene constraint
- LOEUF 0.638 · pLI 0.08 (gnomAD)
- Structure
- AlphaFold pLDDT 94.06 · 62 PDB
Similar variants
- IDE p.Asn841= 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
- IDE p.Ala650Thr 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-his10 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown