LAMB1 p.Ala1069=
c.3207G>A · rs767695883 · VCV2657937
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00445%, eas)
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 -20 | GERP -5.8 |
| Overall | ||
| CADD | 0.673 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00445%
East Asian · 2/44,898 alleles
Filtering AF
0.000738%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000276%
Overall
0.00062%
10/1,613,946 alleles · very rare
exomes 9/1,461,684 · genomes 1/152,262 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00445% | 22,449 |
| African / African-American | 0.00133% | 74,952 |
| South Asian | 0.0011% | 91,032 |
| European (non-Finnish) | 0.000508% | 196,661 |
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.Ala1069=
- Coding
- c.3207G>A
- MANE Select
- NM_002291
- dbSNP
- rs767695883
- Type
- single nucleotide variant
- Location
- chr7:107952096 (GRCh38)
- Gene constraint
- LOEUF 0.601 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.99 · 3 PDB
- Residue 1069
- the laminin egf-like 11 domain
Similar variants
- LAMB1 p.Ala1069Val 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.Ala1239Thr Uncertain significance ★★ ⚠ same type
- LAMB1 p.Ala1331Gly 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-ala1069 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown