LIPC p.Ser282=
c.846G>T · VCV3714210
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0505%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -11 | GERP -9.6 |
| Overall | ||
| CADD | 0.049 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0505%
South Asian · 46/91,072 alleles
Filtering AF
0.0389%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0348%
Overall
0.00359%
58/1,613,980 alleles · ultra-rare
exomes 56/1,461,846 · genomes 2/152,134 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0505% | 1,980 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,943 |
| East Asian | 0.00223% | 44,894 |
| European (non-Finnish) | 0.000169% | 590,012 |
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.Ser282=
- Coding
- c.846G>T
- MANE Select
- NM_000236
- Type
- single nucleotide variant
- Location
- chr15:58548367 (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-ser282 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown