LRPPRC p.Ser707=
c.2121C>T · rs777999258 · VCV752149
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.01%, amr)
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 -5.6 | GERP -5.6 |
| Overall | ||
| CADD | 5.086 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.01%
Admixed American · 6/59,926 alleles
Filtering AF
0.00429%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00296%
Overall
0.00348%
56/1,610,816 alleles · ultra-rare
exomes 53/1,458,874 · genomes 3/151,942 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.01% | 9,988 |
| South Asian | 0.00659% | 15,170 |
| Remaining individualsnot grpmax-eligible | 0.00481% | 20,786 |
| European (non-Finnish) | 0.0034% | 29,437 |
| African / African-American | 0.00134% | 74,766 |
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.Ser707=
- Coding
- c.2121C>T
- MANE Select
- NM_133259
- dbSNP
- rs777999258
- Type
- single nucleotide variant
- Location
- chr2:43946202 (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.Ser707Phe Uncertain significance ★ ⚠ same residue
- LRPPRC p.Ser707fs Likely 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
- LRPPRC c.1735+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-ser707 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown