LCP2 p.Pro242=
c.726C>T · VCV4684889
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 8.19%, sas) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.21 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.52 | GERP -1.5, phastCons 0.99 |
| Overall | ||
| CADD | 11.96 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.19%
South Asian · 7,456/91,072 alleles
Filtering AF
8.03%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 7.97%
Overall
5.12%
82,665/1,613,708 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 8.19% | 12 |
| European (non-Finnish) | 5.28% | 19 |
| Remaining individualsnot grpmax-eligible | 4.96% | 20 |
| African / African-American | 4.9% | 20 |
| Middle Eastern | 4.55% | 22 |
| Admixed American | 3.53% | 28 |
| Finnishnot grpmax-eligible | 2.92% | 34 |
| East Asian | 2.49% | 40 |
| Ashkenazi Jewishnot grpmax-eligible | 2.41% | 41 |
| Amishnot grpmax-eligible | 1.86% | 54 |
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
- LCP2
- Protein
- p.Pro242=
- Coding
- c.726C>T
- MANE Select
- NM_005565
- Type
- single nucleotide variant
- Location
- chr5:170266854 (GRCh38)
- Gene constraint
- LOEUF 0.465 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.50 · 5 PDB
- Residue 242
- the 'disordered' region
Similar variants
- LCP2 p.Pro242Ser Uncertain significance ★ ⚠ same residue
- LCP2 p.Arg407Trp Uncertain significance ★★ ⚠ same type
- LCP2 p.Pro328Leu Uncertain significance ★★ ⚠ same type
- LCP2 c.142-18T>C Benign ★★ same type
- LCP2 c.523+16C>T Benign ★★ same type
- LCP2 p.Gln326= Benign ★★ same type
- LCP2 p.Ser410Cys Benign/Likely benign ★★ same type
- LCP2 p.Val188= Benign ★★ 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/lcp2-p-pro242 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown