LPCAT1 p.Arg413=
c.1239G>A · rs145831294 · VCV723828
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.512%, afr)
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 0.21 | GERP -2.4, phastCons 0.98 |
| Overall | ||
| CADD | 9.027 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.512%
African / African-American · 384/75,050 alleles
Filtering AF
0.469%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.453%
Overall
0.0301%
486/1,613,648 alleles · rare
exomes 252/1,461,320 · genomes 234/152,328 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.512% | 195 |
| Middle Eastern | 0.066% | 1,515 |
| Remaining individualsnot grpmax-eligible | 0.048% | 2,083 |
| Admixed American | 0.0333% | 3,001 |
| European (non-Finnish) | 0.0039% | 25,652 |
| Finnishnot grpmax-eligible | 0.00315% | 31,774 |
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
- LPCAT1
- Protein
- p.Arg413=
- Coding
- c.1239G>A
- MANE Select
- NM_024830
- dbSNP
- rs145831294
- Type
- single nucleotide variant
- Location
- chr5:1470865 (GRCh38)
- Gene constraint
- LOEUF 0.564 · pLI 0.53 (gnomAD)
- Structure
- AlphaFold pLDDT 82.85
- Residue 413
- the ef-hand 1 domain
Similar variants
- LPCAT1 p.Arg413Gln Uncertain significance ★ ⚠ same residue
- LPCAT1 p.Arg413Trp Uncertain significance ★ ⚠ same residue
- LPCAT1 p.Ala319Val Uncertain significance ★ ⚠ same type
- LPCAT1 p.Ala327Thr Uncertain significance ★ ⚠ same type
- LPCAT1 p.Ala370Val Uncertain significance ★ ⚠ same type
- LPCAT1 p.Ala487Thr Uncertain significance ★ ⚠ same type
- LPCAT1 p.Ala524Thr Uncertain significance ★ ⚠ same type
- LPCAT1 p.Ala62Thr 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/lpcat1-p-arg413 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown