LARS1 p.Phe300fs
c.900del · VCV4712611
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
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 10 of 32 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7.5 | GERP 2, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- LARS1
- Protein
- p.Phe300fs
- Coding
- c.900del
- MANE Select
- NM_020117
- Type
- Deletion
- Location
- chr5:146157568 (GRCh38)
- Gene constraint
- LOEUF 0.787 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.78 · 8 PDB
- Residue 300
- the 'editing domain' region; an α-helix
Similar variants
- LARS1 c.214-17del Benign/Likely benign ★★ same type
- LARS1 c.2629-13_2629-8del Benign ★★ same type
- LARS1 c.3325+1del Likely pathogenic ★ same type
- LARS1 p.Arg4fs Pathogenic ★ same type
- LARS1 p.Asn963fs Likely pathogenic ★ same type
- LARS1 p.Lys927fs Likely pathogenic ★ same type
- LARS1 p.Phe603_Tyr604insTer Pathogenic ★ same type
- LARS1 p.Tyr46fs 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/lars1-p-phe300fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown