LRPPRC p.Val844=
c.2532C>T · rs150033044 · VCV1153964
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.0033%, 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 0.29 | GERP -2.7 |
| Overall | ||
| CADD | 1.272 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0033%
South Asian · 3/91,030 alleles
Filtering AF
0.000875%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000443%
Overall
0.000806%
13/1,612,688 alleles · very rare
exomes 11/1,460,658 · genomes 2/152,030 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0033% | 30,343 |
| East Asian | 0.00223% | 44,808 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,438 |
| European (non-Finnish) | 0.000679% | 147,381 |
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.Val844=
- Coding
- c.2532C>T
- MANE Select
- NM_133259
- dbSNP
- rs150033044
- Type
- single nucleotide variant
- Location
- chr2:43934851 (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 844
- 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-val844 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown