ILK p.Glu44=
c.132G>A · VCV3528907
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
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 1.2 | GERP 0.91, phastCons 1 |
| Overall | ||
| CADD | 9.183 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,890 alleles
Filtering AF
7.9e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.4e-05%
Overall
0.00031%
5/1,614,206 alleles · very rare
exomes 5/1,461,882 · genomes 0/152,324 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,890 |
| European (non-Finnish) | 0.000339% | 295,010 |
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
- ILK
- Protein
- p.Glu44=
- Coding
- c.132G>A
- MANE Select
- NM_004517
- Type
- single nucleotide variant
- Location
- chr11:6608088 (GRCh38)
- Gene constraint
- LOEUF 0.798 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.13 · 17 PDB
- Residue 44
- the 'interaction with lims1' region
Similar variants
- ILK p.Ala41Val Uncertain significance ★★ ⚠ same type
- ILK p.Arg149Gln Uncertain significance ★★ ⚠ same type
- ILK p.Arg161Cys Uncertain significance ★★ ⚠ same type
- ILK p.Arg161His Uncertain significance ★★ ⚠ same type
- ILK p.Arg334Gln Uncertain significance ★★ ⚠ same type
- ILK p.Arg436Gln Uncertain significance ★★ ⚠ same type
- ILK p.Arg46Cys Uncertain significance ★★ ⚠ same type
- ILK p.Arg59Trp 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/ilk-p-glu44 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown