LIM2 p.Leu19=
c.57G>A · rs142517355 · VCV541269
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.37%, eas)
Conditions
2
Inborn genetic diseases
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 | GERP 1.2, phastCons 1 |
| Overall | ||
| CADD | 12.07 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.37%
East Asian · 614/44,878 alleles
Filtering AF
1.28%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.24%
Overall
0.106%
1,714/1,614,188 alleles · low-frequency
exomes 1,601/1,461,842 · genomes 113/152,346 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.37% | 73 |
| European (non-Finnish) | 0.0847% | 1,181 |
| Middle Eastern | 0.0826% | 1,211 |
| Remaining individualsnot grpmax-eligible | 0.0544% | 1,839 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0405% | 2,467 |
| South Asian | 0.0351% | 2,846 |
| African / African-American | 0.0133% | 7,507 |
| Finnishnot grpmax-eligible | 0.00781% | 12,800 |
| Admixed American | 0.005% | 20,010 |
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
- LIM2
- Protein
- p.Leu19=
- Coding
- c.57G>A
- MANE Select
- NM_001161748
- dbSNP
- rs142517355
- Type
- single nucleotide variant
- Location
- chr19:51387387 (GRCh38)
- Gene constraint
- LOEUF 1.079 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.11 · 1 PDB
- Residue 19
- an α-helix
Similar variants
- LIM2 p.Arg130Cys Pathogenic/Likely pathogenic ★★ same condition
- LIM2 c.175+113G>C Uncertain significance ★★ same condition
- LIM2 c.175+28G>A Uncertain significance ★★ same condition
- LIM2 p.Ala153Thr Uncertain significance ★★ ⚠ same condition
- LIM2 p.Arg129Cys Uncertain significance ★★ ⚠ same condition
- LIM2 p.Arg162Trp Uncertain significance ★★ ⚠ same condition
- LIM2 p.Arg167Gln Uncertain significance ★★ ⚠ same condition
- LIM2 p.Arg168Cys Uncertain significance ★★ ⚠ same condition
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/lim2-p-leu19 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown