LAMC2 p.Asp662=
c.1986C>T · rs138941174 · VCV721000
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.305%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.79 | GERP -0.03, phastCons 1 |
| Overall | ||
| CADD | 6.645 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.305%
African / African-American · 229/75,024 alleles
Filtering AF
0.273%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.26%
Overall
0.0189%
305/1,614,058 alleles · rare
exomes 155/1,461,780 · genomes 150/152,278 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.305% | 328 |
| Middle Eastern | 0.0502% | 1,993 |
| Remaining individualsnot grpmax-eligible | 0.0496% | 2,016 |
| Admixed American | 0.04% | 2,501 |
| South Asian | 0.0022% | 45,537 |
| European (non-Finnish) | 0.00136% | 73,751 |
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
- LAMC2
- Protein
- p.Asp662=
- Coding
- c.1986C>T
- MANE Select
- NM_005562
- dbSNP
- rs138941174
- Type
- single nucleotide variant
- Location
- chr1:183232315 (GRCh38)
- Gene constraint
- LOEUF 0.797 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 72.89
- Residue 662
- the 'domain ii and i' region
Similar variants
- LAMC2 c.1715-2A>G Likely pathogenic ★★ same type
- LAMC2 c.268+1G>A Likely pathogenic ★★ same type
- LAMC2 c.3328+1G>A Pathogenic/Likely pathogenic ★★ same type
- LAMC2 c.640+1G>A Likely pathogenic ★★ same type
- LAMC2 p.Arg1129Ter Pathogenic ★★ same type
- LAMC2 p.Arg115Ter Pathogenic ★★ same type
- LAMC2 p.Arg170Ter Pathogenic/Likely pathogenic ★★ same type
- LAMC2 p.Arg223Ter 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/lamc2-p-asp662 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown