LAMB3 p.Trp470Ter
c.1410G>A · rs2464831400 · VCV2094416
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
junctional epidermolysis bullosa, non-Herlitz type
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 12 of 23 |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 6 | GERP 1, phastCons 1 |
| Overall | ||
| CADD | 42.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- LAMB3
- Protein
- p.Trp470Ter
- Coding
- c.1410G>A
- MANE Select
- NM_000228
- dbSNP
- rs2464831400
- Type
- single nucleotide variant
- Location
- chr1:209627458 (GRCh38)
- Gene constraint
- LOEUF 0.829 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.55
- Residue 470
- the laminin egf-like 4 domain
Similar variants
- LAMB3 c.1132+5G>A Pathogenic/Likely pathogenic ★★ same condition
- LAMB3 c.1133-22G>A Pathogenic ★★ same condition
- LAMB3 c.1288+1G>T Pathogenic/Likely pathogenic ★★ same condition
- LAMB3 c.1597+1G>T Likely pathogenic ★★ same condition
- LAMB3 c.2701+2T>C Likely pathogenic ★★ same condition
- LAMB3 c.28+1G>T Likely pathogenic ★★ same condition
- LAMB3 c.3228+1G>A Pathogenic ★★ same condition
- LAMB3 c.3383-1G>A Pathogenic/Likely 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-trp470ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown