ILK p.Ala393=
c.1179T>C · VCV4038518
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00178%, nfe)
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 0.61 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 9.317 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00178%
European (non-Finnish) · 21/1,180,032 alleles
Filtering AF
0.00114%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000971%
Overall
0.0013%
21/1,614,094 alleles · very rare
exomes 20/1,461,880 · genomes 1/152,214 · joint denominator
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.Ala393=
- Coding
- c.1179T>C
- MANE Select
- NM_004517
- Type
- single nucleotide variant
- Location
- chr11:6610248 (GRCh38)
- Gene constraint
- LOEUF 0.798 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.13 · 17 PDB
- Residue 393
- the protein kinase domain; a turn
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-ala393 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown