LIPE p.Ser559=
c.1677G>A · rs35831167 · VCV784550
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0794%, 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 -5.4 | |
| Overall | ||
| CADD | 5.067 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0794%
European (non-Finnish) · 911/1,146,638 alleles
Filtering AF
0.0751%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0734%
Overall
0.0639%
990/1,548,162 alleles · ultra-rare
exomes 933/1,395,954 · genomes 57/152,208 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0794% | 1,259 |
| Remaining individualsnot grpmax-eligible | 0.0622% | 1,608 |
| Admixed American | 0.0272% | 3,670 |
| African / African-American | 0.0233% | 4,291 |
| South Asian | 0.00994% | 10,058 |
| Finnishnot grpmax-eligible | 0.00489% | 20,450 |
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
- LIPE
- Protein
- p.Ser559=
- Coding
- c.1677G>A
- MANE Select
- NM_005357
- dbSNP
- rs35831167
- Type
- single nucleotide variant
- Location
- chr19:42407771 (GRCh38)
- Gene constraint
- LOEUF 0.932 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 64.77 · 1 PDB
- Residue 559
- a β-strand
Similar variants
- LIPE p.Arg305Cys Uncertain significance ★★ ⚠ same type
- LIPE p.Arg821Cys Uncertain significance ★★ ⚠ same type
- LIPE p.Gln150Glu Uncertain significance ★★ ⚠ same type
- LIPE p.Leu1027Met Uncertain significance ★★ ⚠ same type
- LIPE p.Leu777Phe Uncertain significance ★★ ⚠ same type
- LIPE p.Val1014Met Uncertain significance ★★ ⚠ same type
- LIPE c.2365+181T>A Benign ★★ same type
- LIPE c.2968-44C>G Benign ★★ 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/lipe-p-ser559 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown