LRPPRC p.Arg13=
c.39T>G · rs1675040850 · VCV1116638
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.77e-05%, 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 -2.3 | GERP -4.3 |
| Overall | ||
| CADD | 0.952 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.77e-05%
European (non-Finnish) · 1/1,139,672 alleles
Overall
6.59e-05%
1/1,516,304 alleles · very rare
exomes 1/1,364,070 · genomes 0/152,234 · joint denominator
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.Arg13=
- Coding
- c.39T>G
- MANE Select
- NM_133259
- dbSNP
- rs1675040850
- Type
- single nucleotide variant
- Location
- chr2:43995909 (GRCh38)
- Gene constraint
- LOEUF 0.808 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 77.35 · 2 PDB
Similar variants
- LRPPRC p.Arg13Gly Uncertain significance ★ ⚠ same residue
- LRPPRC p.Arg13Pro Uncertain significance ★ ⚠ same residue
- LRPPRC p.Arg13fs Pathogenic ★ same residue
- 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
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-arg13 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown