LAMB1 p.Ala559=
c.1677G>A · rs201444455 · VCV774130
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.188%, amr)
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 -10 | GERP -4.1 |
| Overall | ||
| CADD | 0.456 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.188%
Admixed American · 113/60,016 alleles
Filtering AF
0.16%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.149%
Overall
0.0143%
231/1,614,148 alleles · rare
exomes 164/1,461,860 · genomes 67/152,288 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.188% | 531 |
| Middle Eastern | 0.099% | 1,010 |
| South Asian | 0.0198% | 5,060 |
| European (non-Finnish) | 0.00729% | 13,721 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,626 |
| East Asian | 0.00446% | 22,437 |
| African / African-American | 0.00267% | 37,522 |
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
- LAMB1
- Protein
- p.Ala559=
- Coding
- c.1677G>A
- MANE Select
- NM_002291
- dbSNP
- rs201444455
- Type
- single nucleotide variant
- Location
- chr7:107964573 (GRCh38)
- Gene constraint
- LOEUF 0.601 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.99 · 3 PDB
- Residue 559
- the laminin iv type b domain
Similar variants
- LAMB1 p.Ala559Val Uncertain significance ★ ⚠ same residue
- LAMB1 c.4188+1G>C Pathogenic/Likely pathogenic ★★ same type
- LAMB1 p.Arg397Ter Pathogenic ★★ same type
- LAMB1 p.Gln577Ter Pathogenic ★★ same type
- LAMB1 c.1985+5G>T Uncertain significance ★★ same type
- LAMB1 c.4746-3C>A Uncertain significance ★★ same type
- LAMB1 p.Ala1069Val Uncertain significance ★★ ⚠ same type
- LAMB1 p.Ala1239Thr 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/lamb1-p-ala559 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown