LIMK1 p.Pro189=
c.567G>A · rs143025582 · VCV2657584
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.01%, amr)
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 -5 | GERP -9.3 |
| Overall | ||
| CADD | 0.458 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.01%
Admixed American · 6/60,014 alleles
Filtering AF
0.00428%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00321%
Overall
0.00441%
71/1,610,268 alleles · very rare
exomes 59/1,457,988 · genomes 12/152,280 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.01% | 10,002 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,619 |
| European (non-Finnish) | 0.00458% | 21,852 |
| African / African-American | 0.004% | 25,014 |
| South Asian | 0.00329% | 30,361 |
| Finnishnot grpmax-eligible | 0.00166% | 60,212 |
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.Pro189=
- Coding
- c.567G>A
- MANE Select
- NM_002314
- dbSNP
- rs143025582
- Type
- single nucleotide variant
- Location
- chr7:74099197 (GRCh38)
- Gene constraint
- LOEUF 0.338 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 76.07 · 12 PDB
- Residue 189
- the pdz domain
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-pro189 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown