LPL p.Tyr394=
c.1182C>T · rs1330906485 · VCV2039065
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
Conditions
1
Cardiovascular phenotype
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 · C>G here scores Δ0.23 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.27 | GERP 0.71, phastCons 0.98 |
| Overall | ||
| CADD | 5.962 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,060 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000186%
3/1,613,958 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,060 |
| European (non-Finnish) | 0.00017% | 589,957 |
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
- LPL
- Protein
- p.Tyr394=
- Coding
- c.1182C>T
- MANE Select
- NM_000237
- dbSNP
- rs1330906485
- Type
- single nucleotide variant
- Location
- chr8:19960943 (GRCh38)
- Gene constraint
- LOEUF 1.075 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.36 · 5 PDB
- Residue 394
- a β-strand; the plat domain
Similar variants
- LPL c.1019-2A>T Pathogenic ★★ same condition
- LPL c.1139+1G>A Likely pathogenic ★★ same condition
- LPL c.1322+1G>C Pathogenic/Likely pathogenic ★★ same condition
- LPL c.249+1G>A Pathogenic ★★ same condition
- LPL p.Ala98Thr Pathogenic/Likely pathogenic ★★ ⚠ same condition
- LPL p.Arg197Cys Likely pathogenic ★★ same condition
- LPL p.Asp277Asn Pathogenic/Likely pathogenic ★★ same condition
- LPL p.Gln133Ter Pathogenic/Likely pathogenic ★★ 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/lpl-p-tyr394 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown