LRPPRC p.Ala673fs
c.2012dup · VCV4850626
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
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. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 20 of 38 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -0.3 | GERP -5.6, phastCons 0.33 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- LRPPRC
- Protein
- p.Ala673fs
- Coding
- c.2012dup
- MANE Select
- NM_133259
- Type
- Duplication
- Location
- chr2:43947323 (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 p.Asn1190fs Likely pathogenic ★★ same condition
- LRPPRC p.Gly1050fs Pathogenic ★★ same condition
- LRPPRC p.His791fs Pathogenic/Likely pathogenic ★★ same condition
- LRPPRC p.Leu1259fs Pathogenic/Likely pathogenic ★★ same condition
- LRPPRC p.Lys1338Ter Pathogenic/Likely pathogenic ★★ same condition
- LRPPRC p.Phe1222fs Pathogenic/Likely pathogenic ★★ same condition
- LRPPRC p.Ala1105fs Likely pathogenic ★ same condition
- LRPPRC p.Ala517fs 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-p-ala673fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown