LAMB3 p.Pro425=
c.1275G>T · rs148726330 · VCV741305
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0112%, 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 -3.9 |
| Overall | ||
| CADD | 0.415 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0112%
East Asian · 5/44,544 alleles
Filtering AF
0.00437%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00278%
Overall
0.00318%
51/1,605,240 alleles · ultra-rare
exomes 41/1,453,014 · genomes 10/152,226 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0112% | 8,909 |
| European (non-Finnish) | 0.00349% | 28,676 |
| Remaining individualsnot grpmax-eligible | 0.00322% | 31,027 |
| Admixed American | 0.00169% | 59,324 |
| African / African-American | 0.00134% | 74,720 |
| South Asian | 0.00112% | 89,406 |
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.Pro425=
- Coding
- c.1275G>T
- MANE Select
- NM_000228
- dbSNP
- rs148726330
- Type
- single nucleotide variant
- Location
- chr1:209628048 (GRCh38)
- Gene constraint
- LOEUF 0.829 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.55
- Residue 425
- the laminin egf-like 3 domain
Similar variants
- LAMB3 p.Pro425Leu Uncertain significance ★ ⚠ same residue
- LAMB3 c.1132+5G>A Pathogenic/Likely pathogenic ★★ same type
- LAMB3 c.1133-22G>A Pathogenic ★★ same type
- LAMB3 c.1288+1G>T Pathogenic/Likely pathogenic ★★ same type
- LAMB3 c.1486-1G>A Likely pathogenic ★★ same type
- LAMB3 c.1597+1G>T Likely pathogenic ★★ same type
- LAMB3 c.2138-1G>A Likely pathogenic ★★ same type
- LAMB3 c.2701+2T>C 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/lamb3-p-pro425 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown