LPP p.Ile196=
c.588C>T · rs55674610 · VCV775935
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.25%, eas)
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 -5.9 | GERP -5 |
| Overall | ||
| CADD | 3.134 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.25%
East Asian · 561/44,862 alleles
Filtering AF
1.16%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.13%
Overall
0.153%
2,473/1,614,102 alleles · low-frequency
exomes 2,269/1,461,876 · genomes 204/152,226 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.25% | 80 |
| Admixed American | 0.155% | 645 |
| Remaining individualsnot grpmax-eligible | 0.149% | 672 |
| European (non-Finnish) | 0.136% | 737 |
| South Asian | 0.0747% | 1,339 |
| African / African-American | 0.0533% | 1,876 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0203% | 4,933 |
| Finnishnot grpmax-eligible | 0.0172% | 5,821 |
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.Ile196=
- Coding
- c.588C>T
- MANE Select
- NM_001375462
- dbSNP
- rs55674610
- Type
- single nucleotide variant
- Location
- chr3:188609319 (GRCh38)
- Gene constraint
- LOEUF 0.765 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 60.99
- Residue 196
- the 'disordered' region
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-ile196 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown