LIPC p.Pro111=
c.333G>A · rs113496365 · VCV735637
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.368%, afr)
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 -0.037 | GERP -7.5 |
| Overall | ||
| CADD | 6.543 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.368%
African / African-American · 276/75,044 alleles
Filtering AF
0.332%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.318%
Overall
0.028%
452/1,612,974 alleles · rare
exomes 282/1,460,682 · genomes 170/152,292 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.368% | 272 |
| Remaining individualsnot grpmax-eligible | 0.04% | 2,498 |
| Middle Eastern | 0.0165% | 6,060 |
| Admixed American | 0.0133% | 7,497 |
| European (non-Finnish) | 0.0115% | 8,676 |
| South Asian | 0.00549% | 18,206 |
| Finnishnot grpmax-eligible | 0.00159% | 63,082 |
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.Pro111=
- Coding
- c.333G>A
- MANE Select
- NM_000236
- dbSNP
- rs113496365
- Type
- single nucleotide variant
- Location
- chr15:58541844 (GRCh38)
- Gene constraint
- LOEUF 1.102 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.03
Similar variants
- LIPC p.Pro111Leu 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-pro111 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown