Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Common
common (popmax 25.7%, eas) — too common for a highly-penetrant pathogenic allele
Conditions
1
junctional epidermolysis bullosa
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 -20 | GERP -4.2 |
| Overall | ||
| CADD | 2.077 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
25.7%
East Asian · 10,723/41,668 alleles
Filtering AF
25.3%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 25.2%
Overall
2.25%
35,090/1,561,816 alleles · common
exomes 26,146/1,409,566 · genomes 8,944/152,250 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 25.7% | 4 |
| Admixed American | 16.3% | 6 |
| African / African-American | 13.2% | 8 |
| Remaining individualsnot grpmax-eligible | 3.33% | 30 |
| Middle Eastern | 2.83% | 35 |
| South Asian | 1.51% | 66 |
| Finnishnot grpmax-eligible | 0.462% | 216 |
| Ashkenazi Jewishnot grpmax-eligible | 0.254% | 394 |
| European (non-Finnish) | 0.198% | 505 |
| Amishnot grpmax-eligible | 0.11% | 912 |
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
- LAMB3
- Protein
- p.Pro383=
- Coding
- c.1149G>A
- MANE Select
- NM_000228
- dbSNP
- rs2076351
- Type
- single nucleotide variant
- Location
- chr1:209628174 (GRCh38)
- Gene constraint
- LOEUF 0.829 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.55
- Residue 383
- the laminin egf-like 3 domain
Similar variants
- LAMB3 c.1132+5G>A Pathogenic/Likely pathogenic ★★ same condition
- LAMB3 c.1486-1G>A Likely pathogenic ★★ same condition
- LAMB3 c.3228+1G>A Pathogenic ★★ same condition
- LAMB3 c.565-2A>G Pathogenic ★★ same condition
- LAMB3 c.628+1G>A Pathogenic/Likely pathogenic ★★ same condition
- LAMB3 c.823-1G>A Pathogenic ★★ same condition
- LAMB3 p.Arg144Ter Pathogenic ★★ same condition
- LAMB3 p.Arg635Ter Pathogenic ★★ same condition
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/lamb3-p-pro383 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown