LRPPRC c.3151del
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no gnomAD frequency available for this variant
Conditions
1
congenital lactic acidosis, Saguenay-Lac-Saint-Jean type
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 8.7 | GERP 0.99, phastCons 1 |
| Non-coding constraint | Z 0.65 | 1 kb window · o/e 0.95 · regional · uncalibrated |
Population frequency
dbSNP / gnomAD
No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- LRPPRC
- Coding
- c.3151del
- MANE Select
- NM_133259
- dbSNP
- rs2466424623
- Type
- Deletion
- Location
- chr2:43912556 (GRCh38)
- Gene constraint
- LOEUF 0.808 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 77.35 · 2 PDB
Disease context
congenital lactic acidosis, Saguenay-Lac-Saint-Jean type — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Congenital lactic acidosis, Saguenay-Lac-Saint-Jean type (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Infancy, Neonatal
Similar variants
- LRPPRC c.1730_1735+1del Likely pathogenic ★★ same condition
- LRPPRC c.3710-1del Likely pathogenic ★★ same condition
- LRPPRC p.Ala1051fs Pathogenic/Likely pathogenic ★★ same condition
- LRPPRC p.Ala42fs Pathogenic/Likely pathogenic ★★ same condition
- LRPPRC p.Asn1246fs Pathogenic/Likely pathogenic ★★ same condition
- LRPPRC p.Asn454fs Pathogenic/Likely pathogenic ★★ same condition
- LRPPRC p.Gln1005fs Likely pathogenic ★★ same condition
- LRPPRC p.Glu366fs Pathogenic/Likely pathogenic ★★ same condition
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-c-3151del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown