LARS2 p.Pro892=
c.2676G>A · rs550066510 · VCV681429
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0357%, eas)
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 -3.8 | GERP -4.3 |
| Overall | ||
| CADD | 5.52 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0357%
East Asian · 16/44,768 alleles
Filtering AF
0.0224%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0182%
Overall
0.00143%
23/1,612,362 alleles · ultra-rare
exomes 21/1,460,146 · genomes 2/152,216 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0357% | 2,798 |
| African / African-American | 0.00134% | 74,874 |
| South Asian | 0.0011% | 90,810 |
| European (non-Finnish) | 0.000424% | 235,881 |
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
- LARS2
- Protein
- p.Pro892=
- Coding
- c.2676G>A
- MANE Select
- NM_015340
- dbSNP
- rs550066510
- Type
- single nucleotide variant
- Location
- chr3:45547494 (GRCh38)
- Gene constraint
- LOEUF 0.808 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.57
Similar variants
- LARS2 p.Pro892Leu Uncertain significance ★ ⚠ same residue
- LARS2 c.235-2A>G Likely pathogenic ★★ same type
- LARS2 p.Arg228His Likely pathogenic ★★ same type
- LARS2 p.Arg663Trp Pathogenic/Likely pathogenic ★★ same type
- LARS2 p.Arg66Ter Pathogenic/Likely pathogenic ★★ same type
- LARS2 p.Asn153His Pathogenic/Likely pathogenic ★★ same type
- LARS2 p.Asp438Gly Likely pathogenic ★★ ⚠ same type
- LARS2 p.Gln147Pro 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/lars2-p-pro892 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown