PNLIP p.Pro63=
c.189A>C · rs118052168 · VCV2047003
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.116%, amr)
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 -0.33 | GERP 0.7 |
| Overall | ||
| CADD | 3.684 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.116%
Admixed American · 69/59,550 alleles
Filtering AF
0.0939%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0858%
Overall
0.0466%
752/1,612,094 alleles · rare
exomes 669/1,459,882 · genomes 83/152,212 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.116% | 863 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0986% | 1,014 |
| European (non-Finnish) | 0.0498% | 2,009 |
| Remaining individualsnot grpmax-eligible | 0.0385% | 2,598 |
| South Asian | 0.0375% | 2,668 |
| African / African-American | 0.0107% | 9,351 |
| Finnishnot grpmax-eligible | 0.00156% | 63,988 |
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
- PNLIP
- Protein
- p.Pro63=
- Coding
- c.189A>C
- MANE Select
- NM_000936
- dbSNP
- rs118052168
- Type
- single nucleotide variant
- Location
- chr10:116547436 (GRCh38)
- Gene constraint
- LOEUF 0.984 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.84 · 4 PDB
- Residue 63
- a β-strand
Similar variants
- PNLIP p.Pro63Ser Uncertain significance ★ ⚠ same residue
- PNLIP p.Ala13Val Uncertain significance ★★ ⚠ same type
- PNLIP p.Ala71Thr Uncertain significance ★★ ⚠ same type
- PNLIP p.Arg54His Uncertain significance ★★ ⚠ same type
- PNLIP p.Asn183Ser Uncertain significance ★★ ⚠ same type
- PNLIP p.Asn382Ser Uncertain significance ★★ ⚠ same type
- PNLIP p.Cys20Phe Uncertain significance ★★ ⚠ same type
- PNLIP p.Gly157Asp 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/pnlip-p-pro63 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown