LAMC3 p.Arg784=
c.2352G>A · rs35654564 · VCV211364
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.09%, afr)
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 0.033 | GERP -1.5, phastCons 0.53 |
| Overall | ||
| CADD | 5.582 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.09%
African / African-American · 1,565/75,048 alleles
Filtering AF
2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.96%
Overall
0.104%
1,682/1,613,776 alleles · low-frequency
exomes 775/1,461,440 · genomes 907/152,336 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.09% | 48 |
| Admixed American | 0.095% | 1,053 |
| Remaining individualsnot grpmax-eligible | 0.0848% | 1,179 |
| Middle Eastern | 0.0165% | 6,062 |
| South Asian | 0.0022% | 45,542 |
| European (non-Finnish) | 0.000339% | 295,011 |
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.Arg784=
- Coding
- c.2352G>A
- MANE Select
- NM_006059
- dbSNP
- rs35654564
- Type
- single nucleotide variant
- Location
- chr9:131066964 (GRCh38)
- Gene constraint
- LOEUF 0.909 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.23
- Residue 784
- the laminin egf-like 7 domain
Similar variants
- LAMC3 p.Arg784Gln Uncertain significance ★★ ⚠ same residue
- LAMC3 p.Arg784Trp Uncertain significance ★★ ⚠ 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-arg784 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown