# NM_000228.3(LAMB3):c.15C>T (p.Phe5=)

https://sugi.bio/variant/lamb3-p-phe5

## Summary

**LAMB3 p.Phe5= (c.15C>T)** is classified **Conflicting classifications of pathogenicity** in LAMB3 (ClinVar, Conflicting submitters, 4 submitters; last evaluated 2026-01-26). Rare (popmax 0.258%, amr); Associated with junctional epidermolysis bullosa.

**At a glance:** Conflicting classifications of pathogenicity · review: Conflicting submitters · rsID rs140470350 · 4 submitters · 1 linked condition · rare (popmax 0.258%, amr)

## For patients & families {#patients}

This is a change in the LAMB3 gene that is of uncertain or conflicting significance (submitters disagree on it), submitted by 4 submitters, and is linked to junctional epidermolysis bullosa.

*Reference information, not medical advice, and not a prediction for any individual. A genetic counselor or clinician can interpret what it means for you and your family.*

|  |  |
| --- | --- |
| Clinical trials | 15 registered for this condition — see ClinicalTrials.gov |

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0002152/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [LAMB3](https://sugi.bio/atlas/gene/LAMB3/) |
| Protein change (HGVS p.) | p.Phe5= |
| Coding change (HGVS c.) | c.15C>T |
| MANE Select transcript | [NM_000228](https://www.ncbi.nlm.nih.gov/nuccore/NM_000228) |
| dbSNP | [rs140470350](https://www.ncbi.nlm.nih.gov/snp/rs140470350/) |
| Variant type | single nucleotide variant |
| Location | chr1:209650930-209650930 (GRCh38) |
| ClinVar | [VCV782082](https://www.ncbi.nlm.nih.gov/clinvar/variation/782082/) |

**All HGVS expressions:** `NC_000001.10:g.209824275G>A`, `NC_000001.11:g.209650930G>A`, `NG_007116.1:g.6546C>T`, `NM_000228.3:c.15C>T`, `NM_001017402.2:c.15C>T`, `NM_001127641.1:c.15C>T`

## Computational & population evidence {#evidence}

**Concordance:** Mixed / partial computational evidence (see below).

- **Missense predictors (AlphaMissense/REVEL/SaProt) do not apply** to this variant type — they score amino-acid substitutions only. For non-missense variants the computational signal comes from conservation (below), not from a missing predictor score.
- Conservation: phyloP -0.742, GERP -2.87 — not a conserved position (phyloP < 0.1, ACGS BP7 cut)
- CADD: **PHRED 0.567**. No single ClinGen-calibrated threshold exists and the expert panels that use CADD disagree — GUCY2D/AIPL1 require ≥ 20.0 for an untranslated-region variant, ABCA4 ≥ 28.1 for a synonymous or indel variant, the Pulmonary Hypertension panel imports Pejaver 2022's missense-calibrated numbers, and the Antibody Deficiencies panel declines CADD entirely for PIK3CD. CADD v1.7 also incorporates Zoonomia phyloP, so it partly re-expresses the conservation above. *Descriptive; no threshold applied.*
- SpliceAI: **not assessed** — no allele at this position is in our SpliceAI release, either because it lies outside the scored MANE transcript scope or because every allele is below Δ0.2. We cannot tell which, so this claims neither; absence is not evidence against a splicing effect.
- Pangolin: Δ**0.20** (loss), gain 0.00 / loss 0.20. Not in the SpliceAI release. An independent predictor to SpliceAI — a different model trained on different data. *Descriptive; ClinGen's SVI calibration covers SpliceAI, not Pangolin, so no ACMG code is assigned.*
- Population frequency (gnomAD v4.1): grpmax **0.258%** (amr) · FAF95 0.225% · FAF99 0.212% · 155/60,026 in the highest group · 3,278/1,614,134 alleles overall — rare (popmax 0.258%, amr).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Ashkenazi Jewish (not grpmax-eligible) | 0.79% | 127 |
| Admixed American (grpmax) | 0.258% | 387 |
| Remaining individuals (not grpmax-eligible) | 0.243% | 411 |
| European (non-Finnish) | 0.22% | 454 |
| South Asian | 0.0692% | 1,446 |
| Finnish (not grpmax-eligible) | 0.0687% | 1,455 |
| African / African-American | 0.0427% | 2,345 |
| Middle Eastern | 0.0165% | 6,062 |

Ashkenazi Jewish shows a higher raw frequency than the grpmax group. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and "Remaining individuals" — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

*Computational predictors are not independent (ClinGen Variant Classification guidance): AlphaMissense (Cheng et al. 2023) carries the ACMG weight for missense and conservation (phyloP/GERP/phastCons) for non-missense; REVEL (Pejaver-2022 calibrated strength bands) and SaProt (Su et al. 2023, structure-aware, ClinVar-independent protein language model, raw LLR) are shown as orthogonal agreement signals, not additive. For frequency, the gnomAD v4.1 grpmax filtering allele frequency (FAF95) is ClinGen's designated BA1/BS1 input (gnomAD v4 guidance v3.0, June 2025); BA1/BS1 thresholds are disease-specific, not a blanket 5%. Predictions, not a clinical determination.*

## Gene constraint & dosage {#gene-context}

**LAMB3** population constraint: LOEUF 0.829, pLI 6.2848e-23, missense-Z 0.88919. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

## Protein context {#protein}


AlphaFold model confidence (whole protein): pLDDT 78.55, 23% of residues very-high.

## What this gene does {#gene-function}

*Describes the biological roles of LAMB3 (the gene this variant disrupts) — not effects measured for this specific variant. A damaging variant is expected to affect these functions and pathways; the degree depends on the variant.*

**How this variant is thought to act:** LAMB3 participates in disease-associated pathways. In Reactome, LAMB3 is annotated in disease pathway(s) including **Attachment of bacteria to epithelial cells**.

**Disease mechanism (Reactome):** LAMB3 loss or alteration is curated in [Attachment of bacteria to epithelial cells](https://reactome.org/content/detail/R-HSA-9638630).

### Pathways affected {#pathways}

LAMB3 participates in **11 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| ⚕ [Attachment of bacteria to epithelial cells](https://reactome.org/content/detail/R-HSA-9638630) | curated |
| [Anchoring fibril formation](https://reactome.org/content/detail/R-HSA-2214320) | curated |
| [Assembly of collagen fibrils and other multimeric structures](https://reactome.org/content/detail/R-HSA-2022090) | curated |
| [Developmental Lineage of Pancreatic Ductal Cells](https://reactome.org/content/detail/R-HSA-9925563) | curated |
| [Developmental Lineage of Pancreatic Endocrine Mid Progenitor Cells](https://reactome.org/content/detail/R-HSA-9981148) | curated |
| [MET activates PTK2 signaling](https://reactome.org/content/detail/R-HSA-8874081) | curated |
| [Type I hemidesmosome assembly](https://reactome.org/content/detail/R-HSA-446107) | curated |
| [Degradation of the extracellular matrix](https://reactome.org/content/detail/R-HSA-1474228) | electronic |
| [Formation of the dystrophin-glycoprotein complex (DGC)](https://reactome.org/content/detail/R-HSA-9913351) | electronic |
| [Laminin interactions](https://reactome.org/content/detail/R-HSA-3000157) | electronic |
| [Non-integrin membrane-ECM interactions](https://reactome.org/content/detail/R-HSA-3000171) | electronic |

### Molecular function & processes (GO — experimentally supported) {#go}

**Biological process:** endodermal cell differentiation.

## Clinical significance {#significance}

**Conflicting classifications of pathogenicity** — review status Conflicting submitters *(criteria provided, conflicting classifications)*, last evaluated 2026-01-26.

**Submitter consensus:** conflicting (2 Benign, 1 Uncertain significance, 1 Likely benign).

**Submission history:** 4 submissions (2017–2026); classifications have differed over time.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Illumina Laboratory Services, Illumina | Uncertain significance | criteria provided, single submitter | clinical testing | 2017-04-27 |
| PreventionGenetics, part of Exact Sciences | Benign | no assertion criteria provided | clinical testing | 2020-07-28 |
| Labcorp Genetics (formerly Invitae), Labcorp | Benign | criteria provided, single submitter | clinical testing | 2026-01-26 |
| Blueprint Genetics | Likely benign | criteria provided, single submitter | clinical testing | 2024-11-21 |

## Associated conditions {#conditions}

[junctional epidermolysis bullosa](https://sugi.bio/atlas/disease/junctional-epidermolysis-bullosa/).

**Reported phenotype names (ClinVar):** Junctional epidermolysis bullosa, not provided, LAMB3-related disorder, not specified, LAMB3-related condition, AllHighlyPenetrant, none provided.

## Similar variants {#similar}

Related LAMB3 variant pages (same residue, condition, or type): [LAMB3 c.1132+5G>A](/variant/lamb3-c-1132-plus-5g-a), [LAMB3 c.1486-1G>A](/variant/lamb3-c-1486-minus-1g-a), [LAMB3 c.3228+1G>A](/variant/lamb3-c-3228-plus-1g-a), [LAMB3 c.565-2A>G](/variant/lamb3-c-565-minus-2a-g), [LAMB3 c.628+1G>A](/variant/lamb3-c-628-plus-1g-a), [LAMB3 c.823-1G>A](/variant/lamb3-c-823-minus-1g-a), [LAMB3 p.Arg144Ter](/variant/lamb3-p-arg144ter), [LAMB3 p.Arg635Ter](/variant/lamb3-p-arg635ter).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-14); AlphaMissense (Cheng et al. 2023, © Google DeepMind — CC BY 4.0, built 2026-01-27); REVEL (Ioannidis et al. 2016 — ODbL, built 2026-07-13); SaProt (Su et al. 2023 — MIT, built 2026-10-14); SpliceAI (Illumina — free for non-commercial use, built 2026-10-13); CADD (Rentzsch et al. 2019, University of Washington — free for non-commercial use, built 2026-10-10); Conservation (phyloP/phastCons/GERP) (UCSC hg38 470-way mammal (Hiller Lab) + Ensembl Compara, built 2026-07-12); gnomAD Non-coding Constraint (Gnocchi) (Chen et al. 2024, Broad Institute — CC0, built 2026-10-11); gnomAD Regional Missense Constraint (Broad Institute — CC0, built 2026-10-13); Pangolin (Zeng & Li 2022 — CC BY 4.0, built 2026-10-11); Repeat regions (UCSC — RepeatMasker, TRF, segmental duplications, built 2026-10-11); ClinGen (ClinGen, built 2026-09-22); UniProt (CC BY 4.0); Reactome / GO (CC BY 4.0, built 2026-09-23); MaveDB (per-record license, built 2026-10-11); CIViC (CC0, built 2026-09-22); Orphanet (Orphanet, built 2026-06-12)

*Primary record: NCBI ClinVar (variation 782082). Classifications reflect these databases as of the page's build date and may change. Free reference use — not medical advice; consult the primary submitters and a clinician.*