LIPT2 p.Pro139=
c.417C>A · rs978334424 · VCV3058112
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0105%, afr)
Conditions
1
LIPT2-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.139 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -2.9 | GERP -1.5 |
| Overall | ||
| CADD | 4.984 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0105%
African / African-American · 7/66,950 alleles
Filtering AF
0.00483%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00338%
Overall
0.000494%
7/1,417,964 alleles · ultra-rare
exomes 3/1,265,718 · genomes 4/152,246 · joint denominator
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
- Protein
- p.Pro139=
- Coding
- c.417C>A
- MANE Select
- NM_001144869
- dbSNP
- rs978334424
- Type
- single nucleotide variant
- Location
- chr11:74493287 (GRCh38)
- Gene constraint
- LOEUF 1.954 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.37
- Residue 139
- the bpl/lpl catalytic domain
Disease context
LIPT2-related disorder
Similar variants
- LIPT2 p.Pro139Ser Likely benign ★★ ⚠ same residue
- LIPT2 p.Ala121Val Uncertain significance ★★ ⚠ same type
- LIPT2 p.Ala75Thr Uncertain significance ★★ ⚠ same type
- LIPT2 p.Arg158Cys Uncertain significance ★★ ⚠ same type
- LIPT2 p.Arg2Gln Uncertain significance ★★ ⚠ same type
- LIPT2 p.Asp134Ala Uncertain significance ★★ ⚠ same type
- LIPT2 p.Gln133Glu Uncertain significance ★★ ⚠ same type
- LIPT2 p.Glu207Lys 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-p-pro139 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown