LIPT2 c.467del
Uncertain significance
Multiple submitters
Classification
Uncertain significance
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00196%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.86 | GERP -2.9, phastCons 1 |
| Overall | ||
| CADD | 38.0 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00196%
Admixed American · 1/50,972 alleles
Overall
0.000129%
2/1,549,644 alleles · very rare
exomes 0/1,397,526 · genomes 2/152,118 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00196% | 50,972 |
| Remaining individualsnot grpmax-eligible | 0.00166% | 60,076 |
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
- LIPT2
- Coding
- c.467del
- MANE Select
- NM_001144869
- dbSNP
- rs1864360813
- Type
- Deletion
- Location
- chr11:74492364 (GRCh38)
- Gene constraint
- LOEUF 1.954 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.37
Similar variants
- LIPT2 p.Arg85_Gly87del Uncertain significance ★ same type
- LIPT2 p.Asp24_Gln31del 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/lipt2-c-467del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown