LPIN2 p.Asp40=
c.120T>C · rs143261167 · VCV138127
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
rare (popmax 0.756%, afr)
Conditions
2
autoinflammatory syndrome
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 -1.5 | GERP -0.73 |
| Overall | ||
| CADD | 11.15 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.756%
African / African-American · 567/74,988 alleles
Filtering AF
0.705%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.684%
Overall
0.0406%
655/1,614,086 alleles · rare
exomes 313/1,461,888 · genomes 342/152,198 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.756% | 132 |
| Remaining individualsnot grpmax-eligible | 0.0672% | 1,488 |
| Admixed American | 0.0516% | 1,936 |
| European (non-Finnish) | 0.00127% | 78,668 |
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
- LPIN2
- Protein
- p.Asp40=
- Coding
- c.120T>C
- MANE Select
- NM_001375808
- dbSNP
- rs143261167
- Type
- single nucleotide variant
- Location
- chr18:2960721 (GRCh38)
- Gene constraint
- LOEUF 0.582 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 61.12
- Residue 40
- the 'n-lip' region
Similar variants
- LPIN2 c.1269-2A>G Likely pathogenic ★★ same condition
- LPIN2 c.698+1G>A Likely pathogenic ★★ same condition
- LPIN2 c.699-2A>G Likely pathogenic ★★ same condition
- LPIN2 p.Arg157Ter Pathogenic ★★ same condition
- LPIN2 p.Arg197Ter Pathogenic/Likely pathogenic ★★ same condition
- LPIN2 p.Arg280Ter Pathogenic/Likely pathogenic ★★ same condition
- LPIN2 p.Arg517His Pathogenic/Likely pathogenic ★★ ⚠ same condition
- LPIN2 p.Ser734Leu Pathogenic/Likely pathogenic ★★ same condition
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/lpin2-p-asp40 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown