LAMC3 p.Arg912=
c.2736G>A · rs143868806 · VCV1214553
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0564%, nfe)
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 0.93 | GERP -4.3, phastCons 0.43 |
| Overall | ||
| CADD | 8.8 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0564%
European (non-Finnish) · 665/1,178,174 alleles
Filtering AF
0.0529%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0514%
Overall
0.043%
692/1,610,074 alleles · ultra-rare
exomes 659/1,457,890 · genomes 33/152,184 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0564% | 1,772 |
| Remaining individualsnot grpmax-eligible | 0.0321% | 3,119 |
| African / African-American | 0.00668% | 14,976 |
| Admixed American | 0.00333% | 29,986 |
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.Arg912=
- Coding
- c.2736G>A
- MANE Select
- NM_006059
- dbSNP
- rs143868806
- Type
- single nucleotide variant
- Location
- chr9:131068220 (GRCh38)
- Gene constraint
- LOEUF 0.909 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.23
- Residue 912
- the laminin egf-like 9 domain
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-arg912 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown