LRPPRC p.Leu855=
c.2563T>C · rs749500498 · VCV511278
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00263%, nfe)
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 0.45 | GERP -5.9, phastCons 0.21 |
| Overall | ||
| CADD | 0.454 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00263%
European (non-Finnish) · 31/1,178,110 alleles
Filtering AF
0.00189%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00164%
Overall
0.00199%
32/1,611,828 alleles · very rare
exomes 30/1,459,654 · genomes 2/152,174 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00263% | 38,004 |
| African / African-American | 0.00134% | 74,878 |
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
- LRPPRC
- Protein
- p.Leu855=
- Coding
- c.2563T>C
- MANE Select
- NM_133259
- dbSNP
- rs749500498
- Type
- single nucleotide variant
- Location
- chr2:43934820 (GRCh38)
- Gene constraint
- LOEUF 0.808 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 77.35 · 2 PDB
- Residue 855
- the 'interaction with becn1 and aedes aegypti venom allergen-1' region
Similar variants
- LRPPRC c.1369+1G>C Likely pathogenic ★★ same type
- LRPPRC c.1582+7A>G Likely pathogenic ★★ same type
- LRPPRC c.1677+1G>A Likely pathogenic ★★ same type
- LRPPRC c.1677+1G>T Likely pathogenic ★★ same type
- LRPPRC c.1678-1G>A Likely pathogenic ★★ same type
- LRPPRC c.1735+2T>C Likely pathogenic ★★ same type
- LRPPRC c.1920+1G>T Pathogenic/Likely pathogenic ★★ same type
- LRPPRC c.1965+2T>C Likely pathogenic ★★ 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/lrpprc-p-leu855 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown