Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.916%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -5.4 | GERP -3.9 |
| Overall | ||
| CADD | 7.521 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.916%
European (non-Finnish) · 10,812/1,179,960 alleles
Filtering AF
0.902%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.896%
Overall
0.761%
12,286/1,614,014 alleles · rare
exomes 11,437/1,461,820 · genomes 849/152,194 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.916% | 109 |
| Remaining individualsnot grpmax-eligible | 0.689% | 145 |
| Ashkenazi Jewishnot grpmax-eligible | 0.689% | 145 |
| Finnishnot grpmax-eligible | 0.4% | 250 |
| Middle Eastern | 0.396% | 253 |
| South Asian | 0.311% | 322 |
| Admixed American | 0.282% | 355 |
| African / African-American | 0.14% | 714 |
| East Asian | 0.00446% | 22,434 |
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
- LPP
- Protein
- p.Cys465=
- Coding
- c.1395C>T
- MANE Select
- NM_001375462
- dbSNP
- rs6771786
- Type
- single nucleotide variant
- Location
- chr3:188760267 (GRCh38)
- Gene constraint
- LOEUF 0.765 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 60.99
- Residue 465
- the lim zinc-binding 1 domain
Similar variants
- LPP p.Arg140Trp Uncertain significance ★★ ⚠ same type
- LPP c.1113+51T>C Benign ★★ same type
- LPP c.1240+249G>A Benign ★★ same type
- LPP c.1240+75A>G Benign ★★ same type
- LPP c.1410+155C>T Benign ★★ same type
- LPP c.1410+157T>C Benign ★★ same type
- LPP c.1410+162G>A Benign ★★ same type
- LPP c.1410+165T>C 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/lpp-p-cys465 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown