LRPPRC p.Glu515=
c.1545A>G · rs762413841 · VCV752567
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0469%, 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 6.1 | GERP 1.2, phastCons 1 |
| Overall | ||
| CADD | 6.585 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0469%
East Asian · 21/44,816 alleles
Filtering AF
0.0313%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0263%
Overall
0.00143%
23/1,606,154 alleles · ultra-rare
exomes 20/1,453,978 · genomes 3/152,176 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0469% | 2,134 |
| Admixed American | 0.00333% | 29,997 |
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.Glu515=
- Coding
- c.1545A>G
- MANE Select
- NM_133259
- dbSNP
- rs762413841
- Type
- single nucleotide variant
- Location
- chr2:43960578 (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 515
- an α-helix
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-glu515 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown