LIMK1 p.Pro591=
c.1773C>T · rs782543442 · VCV738041
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00128%, 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 -20 | GERP -3.1 |
| Overall | ||
| CADD | 1.026 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00128%
European (non-Finnish) · 15/1,170,298 alleles
Filtering AF
0.00077%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00061%
Overall
0.00094%
15/1,596,496 alleles · very rare
exomes 15/1,444,490 · genomes 0/152,006 · 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
- LIMK1
- Protein
- p.Pro591=
- Coding
- c.1773C>T
- MANE Select
- NM_002314
- dbSNP
- rs782543442
- Type
- single nucleotide variant
- Location
- chr7:74121041 (GRCh38)
- Gene constraint
- LOEUF 0.338 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 76.07 · 12 PDB
- Residue 591
- the protein kinase domain; an α-helix
Similar variants
- LIMK1 c.292-8C>G Benign ★★ same type
- LIMK1 p.Arg469= Benign/Likely benign ★★ same type
- LIMK1 p.Gly207Asp Likely benign ★★ same type
- LIMK1 p.His259Gln Benign/Likely benign ★★ same type
- LIMK1 p.Ile537= Benign/Likely benign ★★ same type
- LIMK1 p.Lys66Thr Benign ★★ same type
- LIMK1 p.Thr113= Likely benign ★★ same type
- LIMK1 c.882-1G>A 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/limk1-p-pro591 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown