Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0736%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.20 | donor loss · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.7 | GERP -3.7 |
| Overall | ||
| CADD | 0.143 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0736%
South Asian · 67/91,064 alleles
Filtering AF
0.0593%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0542%
Overall
0.0095%
153/1,610,828 alleles · ultra-rare
exomes 132/1,458,570 · genomes 21/152,258 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0736% | 1,359 |
| African / African-American | 0.0253% | 3,950 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,248 |
| East Asian | 0.00892% | 11,212 |
| Finnishnot grpmax-eligible | 0.00656% | 15,249 |
| European (non-Finnish) | 0.00398% | 25,104 |
| Admixed American | 0.00334% | 29,968 |
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
- LAMC3
- Protein
- p.Arg770=
- Coding
- c.2308C>A
- MANE Select
- NM_006059
- dbSNP
- rs3739510
- Type
- single nucleotide variant
- Location
- chr9:131061184 (GRCh38)
- Gene constraint
- LOEUF 0.909 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.23
- Residue 770
- the laminin egf-like 7 domain; a UniProt-annotated variant site (in)
Similar variants
- LAMC3 p.Arg770Gln Uncertain significance ★★ ⚠ same residue
- LAMC3 p.Arg770Gly Benign ★★ same residue
- LAMC3 c.1166-1G>A Likely pathogenic ★★ same type
- LAMC3 c.3211+1G>A Likely pathogenic ★★ same type
- LAMC3 c.3211+2T>C Likely pathogenic ★★ same type
- LAMC3 c.976+1G>A Pathogenic ★★ same type
- LAMC3 p.Cys810Ter Pathogenic ★★ same type
- LAMC3 p.Gln550Ter 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/lamc3-p-arg770 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown