LAMC2 p.Arg857=
c.2569C>A · rs780621237 · VCV1586976
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.26 | donor loss · deltas |
|---|---|---|
| Pangolin | Δ0.37 | loss · gain 0.00 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 4.1 | GERP 1.1, phastCons 1 |
| Overall | ||
| CADD | 7.421 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- LAMC2
- Protein
- p.Arg857=
- Coding
- c.2569C>A
- MANE Select
- NM_005562
- dbSNP
- rs780621237
- Type
- single nucleotide variant
- Location
- chr1:183236572 (GRCh38)
- Gene constraint
- LOEUF 0.797 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 72.89
- Residue 857
- the 'domain ii and i' region
Similar variants
- LAMC2 p.Arg857Pro Benign/Likely benign ★★ same residue
- LAMC2 p.Arg857Gly Uncertain significance ★ ⚠ same residue
- LAMC2 p.Arg857Trp Uncertain significance ★ ⚠ same residue
- LAMC2 c.1715-2A>G Likely pathogenic ★★ same type
- LAMC2 c.268+1G>A Likely pathogenic ★★ same type
- LAMC2 c.3328+1G>A Pathogenic/Likely pathogenic ★★ same type
- LAMC2 c.640+1G>A Likely pathogenic ★★ same type
- LAMC2 p.Arg1129Ter 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/lamc2-p-arg857 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown