PLIN1 p.Thr138=
c.414T>G · rs143954379 · VCV707821
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.182%, mid)
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 -2.5 | GERP -4.8 |
| Overall | ||
| CADD | 1.869 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.182%
Middle Eastern · 11/6,060 alleles
Filtering AF
0.102%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0787%
Overall
0.0582%
940/1,614,090 alleles · rare
exomes 878/1,461,772 · genomes 62/152,318 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.182% | 551 |
| South Asian | 0.0989% | 1,011 |
| European (non-Finnish) | 0.0654% | 1,529 |
| Remaining individualsnot grpmax-eligible | 0.0528% | 1,894 |
| Admixed American | 0.0433% | 2,309 |
| African / African-American | 0.00933% | 10,722 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,600 |
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
- PLIN1
- Protein
- p.Thr138=
- Coding
- c.414T>G
- MANE Select
- NM_002666
- dbSNP
- rs143954379
- Type
- single nucleotide variant
- Location
- chr15:89670164 (GRCh38)
- Gene constraint
- LOEUF 1.201 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 54.52
Similar variants
- PLIN1 p.Thr138Ile Uncertain significance ★ ⚠ same residue
- PLIN1 p.Ala361Glu Uncertain significance ★★ ⚠ same type
- PLIN1 p.Arg125Cys Uncertain significance ★★ ⚠ same type
- PLIN1 p.Glu151Lys Uncertain significance ★★ ⚠ same type
- PLIN1 p.Leu404Phe Uncertain significance ★★ ⚠ same type
- PLIN1 p.Leu90Pro Uncertain significance ★★ ⚠ same type
- PLIN1 p.Thr345Ala Uncertain significance ★★ ⚠ same type
- PLIN1 c.1209+9C>T 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/plin1-p-thr138 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown