LCAT p.Phe306=
c.918T>C · rs1287130448 · VCV2567127
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000137%)
Conditions
1
Cardiovascular phenotype
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.25 | acceptor loss, 5 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3.1 | phastCons 0.97 |
| Overall | ||
| CADD | 12.03 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000137%
Overall
0.000137%
2/1,461,826 alleles · very rare
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
- LCAT
- Protein
- p.Phe306=
- Coding
- c.918T>C
- MANE Select
- NM_000229
- dbSNP
- rs1287130448
- Type
- single nucleotide variant
- Location
- chr16:67940309 (GRCh38)
- Gene constraint
- LOEUF 0.568 · pLI 0.77 (gnomAD)
- Structure
- AlphaFold pLDDT 87.33 · 7 PDB
- Residue 306
- an α-helix
Similar variants
- LCAT p.Arg423Cys Likely pathogenic ★★ ⚠ same condition
- LCAT p.Ala432Thr Uncertain significance ★★ ⚠ same condition
- LCAT p.Asp352Asn Uncertain significance ★★ ⚠ same condition
- LCAT p.Gly128Ser Uncertain significance ★★ ⚠ same condition
- LCAT p.Gly196Arg Uncertain significance ★★ ⚠ same condition
- LCAT p.Gly398Arg Uncertain significance ★★ ⚠ same condition
- LCAT p.Gly5Ser Uncertain significance ★★ ⚠ same condition
- LCAT p.Leu309Val 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/lcat-p-phe306 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown