LRPPRC p.Ser788=
c.2364C>T · rs143672315 · VCV507551
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0294%, afr)
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 5.3 | GERP 2.2, phastCons 1 |
| Overall | ||
| CADD | 8.667 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0294%
African / African-American · 22/74,860 alleles
Filtering AF
0.0199%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0168%
Overall
0.00149%
24/1,613,202 alleles · ultra-rare
exomes 9/1,461,222 · genomes 15/151,980 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0294% | 3,403 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,448 |
| European (non-Finnish) | 8.48e-05% | 1,179,421 |
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.Ser788=
- Coding
- c.2364C>T
- MANE Select
- NM_133259
- dbSNP
- rs143672315
- Type
- single nucleotide variant
- Location
- chr2:43943827 (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 788
- the 'interaction with becn1 and aedes aegypti venom allergen-1' region
Similar variants
- LRPPRC p.Ser788Pro Uncertain significance ★ 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
- LRPPRC c.1735+2T>C Likely pathogenic ★★ same type
- LRPPRC c.1920+1G>T Pathogenic/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-ser788 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown