LIPC p.Pro332=
c.996G>A · VCV3705789
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.158%, 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 -2.9 | GERP -4.9 |
| Overall | ||
| CADD | 2.965 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.158%
South Asian · 142/89,688 alleles
Filtering AF
0.137%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.129%
Overall
0.012%
192/1,602,172 alleles · rare
exomes 172/1,449,862 · genomes 20/152,310 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.158% | 632 |
| African / African-American | 0.024% | 4,165 |
| Admixed American | 0.0139% | 7,194 |
| Remaining individualsnot grpmax-eligible | 0.0129% | 7,760 |
| East Asian | 0.00672% | 14,877 |
| Finnishnot grpmax-eligible | 0.00317% | 31,575 |
| European (non-Finnish) | 0.000937% | 106,724 |
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.Pro332=
- Coding
- c.996G>A
- MANE Select
- NM_000236
- Type
- single nucleotide variant
- Location
- chr15:58548517 (GRCh38)
- Gene constraint
- LOEUF 1.102 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.03
Similar variants
- LIPC p.Pro332Leu 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
- LIPC p.Arg138Cys 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-pro332 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown