LCP2 p.Thr239=
c.717G>A · VCV4973043
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00133%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.20 | acceptor loss · deltas |
|---|---|---|
| Pangolin | Δ0.21 | loss · gain 0.00 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP -7.9 | GERP -3.1 |
| Overall | ||
| CADD | 1.911 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00133%
African / African-American · 1/74,974 alleles
Filtering AF
0.000247%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000159%
Overall
0.000496%
8/1,613,798 alleles · very rare
exomes 8/1,461,656 · genomes 0/152,142 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00133% | 74,974 |
| European (non-Finnish) | 0.000593% | 168,545 |
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.Thr239=
- Coding
- c.717G>A
- MANE Select
- NM_005565
- Type
- single nucleotide variant
- Location
- chr5:170266863 (GRCh38)
- Gene constraint
- LOEUF 0.465 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.50 · 5 PDB
- Residue 239
- an α-helix; the 'disordered' region
Similar variants
- 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.Pro242= 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-thr239 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown