LAMC3 p.Pro1568=
c.4704C>T · rs145337606 · VCV735344
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0225%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.179 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -16 | GERP -3.2 |
| Overall | ||
| CADD | 0.141 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0225%
European (non-Finnish) · 265/1,179,992 alleles
Filtering AF
0.0202%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0194%
Overall
0.0177%
285/1,612,842 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0225% | 4,453 |
| Admixed American | 0.015% | 6,664 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,412 |
| African / African-American | 0.00534% | 18,727 |
| South Asian | 0.0011% | 91,048 |
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.Pro1568=
- Coding
- c.4704C>T
- MANE Select
- NM_006059
- dbSNP
- rs145337606
- Type
- single nucleotide variant
- Location
- chr9:131091763 (GRCh38)
- Gene constraint
- LOEUF 0.909 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.23
- Residue 1568
- the 'domain ii and i' region
Similar variants
- 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
- LAMC3 p.Ala1090Ser Uncertain significance ★★ ⚠ 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-pro1568 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown