LAMC3 p.Pro464=
c.1392G>A · rs776814662 · VCV1200526
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0178%, 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 -20 | GERP -2.8 |
| Overall | ||
| CADD | 0.003 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0178%
East Asian · 8/44,896 alleles
Filtering AF
0.00883%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00641%
Overall
0.00161%
26/1,613,408 alleles · ultra-rare
exomes 24/1,461,214 · genomes 2/152,194 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0178% | 5,612 |
| Admixed American | 0.00667% | 15,002 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,478 |
| South Asian | 0.0011% | 91,080 |
| European (non-Finnish) | 0.00102% | 98,336 |
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.Pro464=
- Coding
- c.1392G>A
- MANE Select
- NM_006059
- dbSNP
- rs776814662
- Type
- single nucleotide variant
- Location
- chr9:131045533 (GRCh38)
- Gene constraint
- LOEUF 0.909 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.23
- Residue 464
- the laminin egf-like 4 domain
Similar variants
- LAMC3 p.Pro464Leu 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
- LAMC3 p.Ser421Ter 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-pro464 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown