LPP p.Ser155=
c.465G>A · rs138963849 · VCV2654351
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.119%, 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 -2.3 | GERP -3 |
| Overall | ||
| CADD | 4.59 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.119%
South Asian · 108/90,930 alleles
Filtering AF
0.101%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0938%
Overall
0.0418%
674/1,610,908 alleles · rare
exomes 638/1,460,916 · genomes 36/149,992 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.119% | 842 |
| Remaining individualsnot grpmax-eligible | 0.0464% | 2,153 |
| European (non-Finnish) | 0.0449% | 2,229 |
| Middle Eastern | 0.0165% | 6,048 |
| Admixed American | 0.00503% | 19,891 |
| Finnishnot grpmax-eligible | 0.00315% | 31,735 |
| African / African-American | 0.0027% | 37,048 |
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.Ser155=
- Coding
- c.465G>A
- MANE Select
- NM_001375462
- dbSNP
- rs138963849
- Type
- single nucleotide variant
- Location
- chr3:188609196 (GRCh38)
- Gene constraint
- LOEUF 0.765 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 60.99
- Residue 155
- the 'disordered' region
Similar variants
- LPP p.Ser155Leu Uncertain significance ★ ⚠ same residue
- 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
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-ser155 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown