LIPC p.Arg333=
c.997C>A · rs142388191 · VCV3017789
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00409%, nfe)
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 0.012 | GERP 3.8 |
| Overall | ||
| CADD | 1.623 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00409%
European (non-Finnish) · 48/1,173,968 alleles
Filtering AF
0.00317%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0028%
Overall
0.00306%
49/1,601,968 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00409% | 24,458 |
| Remaining individualsnot grpmax-eligible | 0.00161% | 62,054 |
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.Arg333=
- Coding
- c.997C>A
- MANE Select
- NM_000236
- dbSNP
- rs142388191
- Type
- single nucleotide variant
- Location
- chr15:58548518 (GRCh38)
- Gene constraint
- LOEUF 1.102 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.03
Similar variants
- LIPC p.Arg333Gln Uncertain significance ★★ ⚠ same residue
- LIPC p.Arg333Trp Uncertain significance ★ ⚠ same residue
- 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
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-arg333 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown