LPL p.Ser21=
c.63C>T · rs772418131 · VCV1654202
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0011%, sas)
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 | GERP -1.2 |
| Overall | ||
| CADD | 12.98 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
South Asian · 1/90,700 alleles
Overall
0.000124%
2/1,610,310 alleles · very rare
exomes 2/1,458,022 · genomes 0/152,288 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0011% | 90,700 |
| European (non-Finnish) | 8.48e-05% | 1,178,906 |
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
- LPL
- Protein
- p.Ser21=
- Coding
- c.63C>T
- MANE Select
- NM_000237
- dbSNP
- rs772418131
- Type
- single nucleotide variant
- Location
- chr8:19939503 (GRCh38)
- Gene constraint
- LOEUF 1.075 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.36 · 5 PDB
Similar variants
- LPL c.1019-2A>T Pathogenic ★★ same type
- LPL c.1019-3C>A Pathogenic/Likely pathogenic ★★ same type
- LPL c.1139+1G>A Likely pathogenic ★★ same type
- LPL c.1139+7A>G Likely pathogenic ★★ same type
- LPL c.1322+1G>C Pathogenic/Likely pathogenic ★★ same type
- LPL c.249+1G>A Pathogenic ★★ same type
- LPL c.89-1G>A Pathogenic/Likely pathogenic ★★ same type
- LPL c.89-1G>C Pathogenic/Likely pathogenic ★★ 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/lpl-p-ser21 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown