LIPC p.Val144=
c.432C>T · VCV3711096
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, mid)
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>A here scores Δ0.55 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.3 | GERP -5.4 |
| Overall | ||
| CADD | 3.854 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,080 alleles
Filtering AF
0.00435%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00329%
Overall
0.00441%
71/1,610,714 alleles · ultra-rare
exomes 67/1,458,514 · genomes 4/152,200 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,080 |
| East Asian | 0.0112% | 8,960 |
| Remaining individualsnot grpmax-eligible | 0.00961% | 10,403 |
| European (non-Finnish) | 0.00466% | 21,449 |
| South Asian | 0.00331% | 30,221 |
| Admixed American | 0.00167% | 59,938 |
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
- LIPC
- Protein
- p.Val144=
- Coding
- c.432C>T
- MANE Select
- NM_000236
- Type
- single nucleotide variant
- Location
- chr15:58541943 (GRCh38)
- Gene constraint
- LOEUF 1.102 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.03
Similar variants
- LIPC c.456+2T>C Uncertain significance ★★ same type
- LIPC c.456+5C>T Uncertain significance ★★ same type
- LIPC p.Ala105Val Uncertain significance ★★ ⚠ same type
- LIPC p.Ala106Val Uncertain significance ★★ ⚠ same type
- LIPC p.Arg135Cys Uncertain significance ★★ ⚠ same type
- LIPC p.Arg135His Uncertain significance ★★ ⚠ same type
- LIPC p.Arg138Cys Uncertain significance ★★ ⚠ same type
- LIPC p.Arg225Gln 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/lipc-p-val144 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown