LIPE p.Tyr960=
c.2880C>T · rs140658352 · VCV719524
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.154%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.31 | acceptor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3 | phastCons 1 |
| Overall | ||
| CADD | 13.86 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.154%
European (non-Finnish) · 1,749/1,136,054 alleles
Filtering AF
0.148%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.145%
Overall
0.123%
1,884/1,531,518 alleles · rare
exomes 1,779/1,379,170 · genomes 105/152,348 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.154% | 650 |
| Remaining individualsnot grpmax-eligible | 0.151% | 660 |
| Admixed American | 0.0466% | 2,145 |
| African / African-American | 0.0248% | 4,029 |
| Finnishnot grpmax-eligible | 0.00656% | 15,253 |
| South Asian | 0.00127% | 78,856 |
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.Tyr960=
- Coding
- c.2880C>T
- MANE Select
- NM_005357
- dbSNP
- rs140658352
- Type
- single nucleotide variant
- Location
- chr19:42402694 (GRCh38)
- Gene constraint
- LOEUF 0.932 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 64.77 · 1 PDB
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-tyr960 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown