LIPE p.Pro995=
c.2985C>T · rs370837760 · VCV435763
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
rare (popmax 0.136%, amr)
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 0.74 | phastCons 1 |
| Overall | ||
| CADD | 12.8 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.136%
Admixed American · 64/47,042 alleles
Filtering AF
0.109%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0996%
Overall
0.0885%
1,332/1,504,350 alleles · rare
exomes 1,223/1,351,972 · genomes 109/152,378 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.136% | 735 |
| European (non-Finnish) | 0.102% | 977 |
| South Asian | 0.0803% | 1,245 |
| Remaining individualsnot grpmax-eligible | 0.0431% | 2,322 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0308% | 3,243 |
| African / African-American | 0.0213% | 4,693 |
| Finnishnot grpmax-eligible | 0.0123% | 8,144 |
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.Pro995=
- Coding
- c.2985C>T
- MANE Select
- NM_005357
- dbSNP
- rs370837760
- Type
- single nucleotide variant
- Location
- chr19:42402058 (GRCh38)
- Gene constraint
- LOEUF 0.932 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 64.77 · 1 PDB
Similar variants
- LIPE p.Pro995Leu Uncertain significance ★ ⚠ same residue
- 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
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-pro995 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown