LAMB1 p.Ser780=
c.2340G>A · VCV4705298
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00483%, 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 -15 | GERP -5 |
| Overall | ||
| CADD | 0.097 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00483%
European (non-Finnish) · 57/1,179,826 alleles
Filtering AF
0.00378%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00345%
Overall
0.00378%
61/1,613,546 alleles · very rare
exomes 57/1,461,326 · genomes 4/152,220 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00483% | 20,699 |
| East Asian | 0.00223% | 44,892 |
| Admixed American | 0.00167% | 59,930 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,476 |
| South Asian | 0.0011% | 90,924 |
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.Ser780=
- Coding
- c.2340G>A
- MANE Select
- NM_002291
- Type
- single nucleotide variant
- Location
- chr7:107959809 (GRCh38)
- Gene constraint
- LOEUF 0.601 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.99 · 3 PDB
- Residue 780
- the laminin egf-like 6 domain
Similar variants
- LAMB1 p.Ser780Leu 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-ser780 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown