PLTP p.Ser78=
c.234C>T · VCV3711908
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0867%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.24 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.9 | GERP -3.8 |
| Overall | ||
| CADD | 4.837 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0867%
South Asian · 79/91,072 alleles
Filtering AF
0.0713%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0657%
Overall
0.00719%
116/1,614,126 alleles · ultra-rare
exomes 106/1,461,778 · genomes 10/152,348 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0867% | 1,153 |
| Remaining individualsnot grpmax-eligible | 0.0176% | 5,683 |
| East Asian | 0.00446% | 22,441 |
| European (non-Finnish) | 0.00186% | 53,635 |
| Finnishnot grpmax-eligible | 0.00156% | 64,034 |
| African / African-American | 0.00133% | 75,054 |
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
- PLTP
- Protein
- p.Ser78=
- Coding
- c.234C>T
- MANE Select
- NM_006227
- Type
- single nucleotide variant
- Location
- chr20:45910037 (GRCh38)
- Gene constraint
- LOEUF 1.002 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.36
Similar variants
- PLTP p.Ala155Thr Uncertain significance ★★ ⚠ same type
- PLTP p.Ala155Val Uncertain significance ★★ ⚠ same type
- PLTP p.Arg177Cys Uncertain significance ★★ ⚠ same type
- PLTP p.Arg251Gln Uncertain significance ★★ ⚠ same type
- PLTP p.Arg372His Uncertain significance ★★ ⚠ same type
- PLTP p.Arg380Gln Uncertain significance ★★ ⚠ same type
- PLTP p.Arg391Cys Uncertain significance ★★ ⚠ same type
- PLTP p.Arg394Pro 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/pltp-p-ser78 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown