LIPT2 p.Ser40=
c.120G>A · rs765093762 · VCV1606541
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0233%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.005 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -2.6 | GERP -3 |
| Overall | ||
| CADD | 4.293 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0233%
Middle Eastern · 1/4,298 alleles
Filtering AF
0.00409%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00238%
Overall
0.000827%
12/1,451,632 alleles · ultra-rare
exomes 11/1,299,456 · genomes 1/152,176 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0233% | 4,298 |
| East Asian | 0.012% | 8,352 |
| South Asian | 0.00538% | 18,571 |
| Remaining individualsnot grpmax-eligible | 0.00537% | 18,636 |
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.Ser40=
- Coding
- c.120G>A
- MANE Select
- NM_001144869
- dbSNP
- rs765093762
- Type
- single nucleotide variant
- Location
- chr11:74493584 (GRCh38)
- Gene constraint
- LOEUF 1.954 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.37
Similar variants
- 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
- LIPT2 p.Gly109Asp 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-ser40 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown