LIMK1 p.Pro336=
c.1008G>A · rs782302735 · VCV745922
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0107%, afr)
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 -13 | GERP -14 |
| Overall | ||
| CADD | 0.076 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0107%
African / African-American · 8/74,946 alleles
Filtering AF
0.00528%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0038%
Overall
0.00192%
31/1,612,968 alleles · ultra-rare
exomes 28/1,460,736 · genomes 3/152,232 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0107% | 9,368 |
| Admixed American | 0.00834% | 11,997 |
| Finnishnot grpmax-eligible | 0.00316% | 31,604 |
| South Asian | 0.0022% | 45,504 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,464 |
| European (non-Finnish) | 0.0011% | 90,761 |
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.Pro336=
- Coding
- c.1008G>A
- MANE Select
- NM_002314
- dbSNP
- rs782302735
- Type
- single nucleotide variant
- Location
- chr7:74107136 (GRCh38)
- Gene constraint
- LOEUF 0.338 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 76.07 · 12 PDB
- Residue 336
- 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-pro336 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown