LAMC2 p.Thr1069=
c.3207G>A · rs748282223 · VCV2416174
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.004%, 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 -0.36 | GERP -3.5 |
| Overall | ||
| CADD | 3.891 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.004%
African / African-American · 3/74,922 alleles
Filtering AF
0.00106%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000495%
Overall
0.000558%
9/1,614,100 alleles · very rare
exomes 8/1,461,890 · genomes 1/152,210 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.004% | 24,974 |
| South Asian | 0.0011% | 91,094 |
| European (non-Finnish) | 0.000424% | 236,009 |
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.Thr1069=
- Coding
- c.3207G>A
- MANE Select
- NM_005562
- dbSNP
- rs748282223
- Type
- single nucleotide variant
- Location
- chr1:183240177 (GRCh38)
- Gene constraint
- LOEUF 0.797 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 72.89
- Residue 1069
- the 'domain ii and i' region
Similar variants
- LAMC2 p.Thr1069Met Benign/Likely benign ★★ same residue
- 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
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-thr1069 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown