Junctional epidermolysis bullosa with pyloric atresia

disease
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Also known as Carmi syndromeepidermolysis bullosa junctionalis with pyloric atresiaepidermolysis bullosa with pyloric atresiaepidermolysis bullosa, junctional, with pyloric stenosisJEB-PAjunctional epidermolysis bullosa - pyloric atresia

Summary

Junctional epidermolysis bullosa with pyloric atresia (MONDO:0009183) is a disease caused by variants in ITGB4 and ITGA6, with 6 cohort genes. The dominant Reactome pathway is Type I hemidesmosome assembly (3 cohort genes).

At a glance

  • Prevalence: <1 / 1 000 000 (Worldwide) [Orphanet-validated]
  • Causal genes: ITGB4 (GenCC Definitive), ITGA6 (GenCC Strong)
  • Cohort genes: 6
  • ClinVar variants: 757
  • Phenotypes (HPO): 21

Clinical features

Epidemiology

Prevalence records

2 prevalence record(s), Orphanet:

TypeClassValueGeographyValidation
Cases/families100WorldwideValidated
Point prevalence<1 / 1 000 000WorldwideValidated

Signs & symptoms

Clinical features (HPO)

21 HPO clinical features (Orphanet curated; top 21 by frequency):

HPO IDTermFrequency
HP:0002017Nausea and vomitingVery frequent (80-99%)
HP:0003270Abdominal distentionVery frequent (80-99%)
HP:0004399Congenital pyloric atresiaVery frequent (80-99%)
HP:0008066Abnormal blistering of the skinVery frequent (80-99%)
HP:0011100Intestinal atresiaVery frequent (80-99%)
HP:0200097Oral mucosal blistersVery frequent (80-99%)
HP:0000070UreteroceleFrequent (30-79%)
HP:0000075Renal duplicationFrequent (30-79%)
HP:0000110Renal dysplasiaFrequent (30-79%)
HP:0000126HydronephrosisFrequent (30-79%)
HP:0000790HematuriaFrequent (30-79%)
HP:0001561PolyhydramniosFrequent (30-79%)
HP:0001581Recurrent skin infectionsFrequent (30-79%)
HP:0006297Enamel hypoplasiaFrequent (30-79%)
HP:0010477Aplasia of the bladderFrequent (30-79%)
HP:0012227Urethral strictureFrequent (30-79%)
HP:0100577Urinary bladder inflammationFrequent (30-79%)
HP:0000656EctropionOccasional (5-29%)
HP:0001057Aplasia cutis congenitaOccasional (5-29%)
HP:0001059PterygiumOccasional (5-29%)
HP:0008404Nail dystrophyOccasional (5-29%)

Identifiers

Disease identifiers

FieldValue
Canonical namejunctional epidermolysis bullosa with pyloric atresia
Mondo IDMONDO:0009183
MeSHC535377
OMIM226730
Orphanet79403
DOIDDOID:0060733
ICD-111877890811
UMLSC5676875
MedGen1810975
GARD0009694
Is cancer (heuristic)no

Also known as: Carmi syndrome · epidermolysis bullosa junctionalis with pyloric atresia · epidermolysis bullosa with pyloric atresia · epidermolysis bullosa, junctional, with pyloric stenosis · JEB-PA · junctional epidermolysis bullosa - pyloric atresia · junctional epidermolysis bullosa with pyloric atresia

Data availability: 757 ClinVar variants · 9 GenCC gene-disease records.

Disease family

Classification path: disease › human disease › disease by body system or component › integumentary system disorder › skin disordervesiculobullous skin diseaseepidermolysis bullosainherited epidermolysis bullosajunctional epidermolysis bullosajunctional epidermolysis bullosa with pyloric atresia

Related subtypes (14): late-onset localized junctional epidermolysis bullosa-intellectual disability syndrome, junctional epidermolysis bullosa, non-Herlitz type, junctional epidermolysis bullosa Herlitz type, laryngo-onycho-cutaneous syndrome, epidermolysis bullosa, junctional 7, with interstitial lung disease and nephrotic syndrome, junctional epidermolysis bullosa inversa, late-onset junctional epidermolysis bullosa, epidermolysis bullosa, junctional 2A, intermediate, epidermolysis bullosa, junctional 2B, severe, epidermolysis bullosa, junctional 3A, intermediate, epidermolysis bullosa, junctional 3B, severe, epidermolysis bullosa, junctional 4, intermediate, epidermolysis bullosa, junctional 5A, intermediate, epidermolysis bullosa, junctional 6, with pyloric atresia

Genetics & variants

GWAS landscape

No GWAS associations recorded — common-variant (GWAS) studies don’t cover this disease (typical for Mendelian / rare diseases). See the curated gene cohort and Mendelian overlap below.

Variant details and genetic-evidence tiers

ClinVar germline variants

600 retrieved; paginated sample, class counts are floors:

335 uncertain significance, 106 conflicting classifications of pathogenicity, 37 benign/likely benign, 36 benign, 30 pathogenic, 25 likely pathogenic, 17 pathogenic/likely pathogenic, 14 likely benign

ClinVarVariant (HGVS)GeneClassificationReview
14731NM_000213.5(ITGB4):c.4620del (p.Thr1542fs)GALK1Pathogeniccriteria provided, single submitter
14737NM_000213.5(ITGB4):c.4643G>A (p.Trp1548Ter)GALK1Pathogenicno assertion criteria provided
14739NM_000213.5(ITGB4):c.3977-19T>AGALK1Pathogeniccriteria provided, single submitter
14742NM_000213.5(ITGB4):c.3841C>T (p.Arg1281Trp)GALK1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
2872718NM_000213.5(ITGB4):c.5058_5064del (p.Ala1687fs)GALK1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
2913409NM_000213.5(ITGB4):c.4355dup (p.Ser1454fs)GALK1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
3002284NM_000213.5(ITGB4):c.5257C>T (p.Gln1753Ter)GALK1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
3256593NM_000213.5(ITGB4):c.4505_4508dup (p.Thr1504fs)GALK1Pathogeniccriteria provided, single submitter
3256594NM_000213.5(ITGB4):c.3842G>C (p.Arg1281Pro)GALK1Pathogeniccriteria provided, single submitter
1179120NM_000210.4(ITGA6):c.915del (p.His305fs)ITGA6Pathogeniccriteria provided, single submitter
1048031NM_000213.5(ITGB4):c.472_566+184delITGB4Pathogeniccriteria provided, single submitter
1048032NM_000213.5(ITGB4):c.701G>T (p.Gly234Val)ITGB4Pathogeniccriteria provided, single submitter
1048060NM_000213.5(ITGB4):c.847C>T (p.Arg283Cys)ITGB4Pathogeniccriteria provided, single submitter
1048061NM_000213.5(ITGB4):c.997T>G (p.Tyr333Asp)ITGB4Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1048062NM_000213.5(ITGB4):c.1370G>A (p.Cys457Tyr)ITGB4Pathogeniccriteria provided, single submitter
1048063NM_000213.5(ITGB4):c.2012G>C (p.Cys671Ser)ITGB4Pathogeniccriteria provided, single submitter
1048064NM_000213.5(ITGB4):c.2465T>C (p.Leu822Ser)ITGB4Pathogeniccriteria provided, single submitter
1048065NM_000213.5(ITGB4):c.2633+1G>AITGB4Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1048066NM_000213.5(ITGB4):c.3040C>T (p.Arg1014Trp)ITGB4Pathogeniccriteria provided, single submitter
1048067NM_000213.5(ITGB4):c.3321_3331del (p.Asp1109fs)ITGB4Pathogeniccriteria provided, multiple submitters, no conflicts
1048068NM_000213.5(ITGB4):c.3707_3725del (p.Thr1236fs)ITGB4Pathogeniccriteria provided, multiple submitters, no conflicts
1180851NM_000213.5(ITGB4):c.1135C>T (p.Arg379Ter)ITGB4Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1252046NM_000213.5(ITGB4):c.3793+1G>CITGB4Pathogeniccriteria provided, single submitter
1292044NM_000213.5(ITGB4):c.794dup (p.Ala266fs)ITGB4Pathogeniccriteria provided, multiple submitters, no conflicts
14730ITGB4, 1-BP DEL, 1150GITGB4Pathogenicno assertion criteria provided
14732NM_000213.5(ITGB4):c.467T>C (p.Leu156Pro)ITGB4Pathogenicno assertion criteria provided
14733NM_000213.5(ITGB4):c.1660C>T (p.Arg554Ter)ITGB4Pathogeniccriteria provided, multiple submitters, no conflicts
14734NM_000213.5(ITGB4):c.182G>A (p.Cys61Tyr)ITGB4Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
14736NM_000213.5(ITGB4):c.3793+1G>AITGB4Pathogeniccriteria provided, multiple submitters, no conflicts
14738NM_000213.5(ITGB4):c.112T>C (p.Cys38Arg)ITGB4Pathogenicno assertion criteria provided

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 18 · Orphanet: 15 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

GenCC gene–disease validity (cohort genes)

the Disease column is the GenCC-asserted condition — a cohort gene’s strongest validity may be for a related predisposition syndrome.

GeneClassificationInheritanceDiseaseRecords
ITGB4DefinitiveAutosomal recessivejunctional epidermolysis bullosa with pyloric atresia14
ITGA6StrongAutosomal recessivejunctional epidermolysis bullosa with pyloric atresia4

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
ITGA6Orphanet:79403Junctional epidermolysis bullosa with pyloric atresia
ITGB4Orphanet:1114Aplasia cutis congenita
ITGB4Orphanet:158684Epidermolysis bullosa simplex with pyloric atresia
ITGB4Orphanet:251393Localized junctional epidermolysis bullosa
ITGB4Orphanet:79402Intermediate generalized junctional epidermolysis bullosa
ITGB4Orphanet:79403Junctional epidermolysis bullosa with pyloric atresia
GALK1Orphanet:79237Galactokinase deficiency
MYO6Orphanet:228012Progressive sensorineural hearing loss-hypertrophic cardiomyopathy syndrome
MYO6Orphanet:90635Rare autosomal dominant non-syndromic sensorineural deafness type DFNA
MYO6Orphanet:90636Rare autosomal recessive non-syndromic sensorineural deafness type DFNB
PLECOrphanet:1114Aplasia cutis congenita
PLECOrphanet:158684Epidermolysis bullosa simplex with pyloric atresia
PLECOrphanet:254361Plectin-related limb-girdle muscular dystrophy R17
PLECOrphanet:257Epidermolysis bullosa simplex with muscular dystrophy
PLECOrphanet:79401PLEC-related intermediate epidermolysis bullosa simplex without extracutaneous involvement

Cohort genes → proteins

6 cohort genes, 5 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence6

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
ITGA6HGNC:6142ENSG00000091409P23229Integrin alpha-6gencc,clinvar
ITGB4HGNC:6158ENSG00000132470P16144Integrin beta-4gencc,clinvar
ITGA6-AS1HGNC:40308ENSG00000232788ITGA6 and PDK1 antisense RNA 1clinvar
GALK1HGNC:4118ENSG00000108479P51570Galactokinaseclinvar
MYO6HGNC:7605ENSG00000196586Q9UM54Unconventional myosin-VIclinvar
PLECHGNC:9069ENSG00000178209Q15149Plectinclinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
ITGA6Integrin alpha-6Integrin alpha-6/beta-1 (ITGA6:ITGB1) is a receptor for laminin on platelets.
ITGB4Integrin beta-4Integrin alpha-6/beta-4 is a receptor for laminin.
GALK1GalactokinaseCatalyzes the transfer of a phosphate from ATP to alpha-D-galactose and participates in the first committed step in the catabolism of galactose.
MYO6Unconventional myosin-VIMyosins are actin-based motor molecules with ATPase activity.
PLECPlectinInterlinks intermediate filaments with microtubules and microfilaments and anchors intermediate filaments to desmosomes or hemidesmosomes.

Protein-family classification

Druggable: 3 · Difficult: 2 · Unknown: 1 · Druggable fraction: 0.5

Family distribution

Cohort families vs a genome-wide background (hypergeometric, BH-FDR; fold = observed/expected). Counts kept; sorted by enrichment, so the catch-all Other/Unknown bucket no longer leads.

FamilyGenesFoldFDR
Antibody/Immunoglobulin29.7×0.064
Scaffold/PPI25.8×0.086
Kinase14.6×0.264
Other/Unknown10.3×0.993

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
ITGA6Antibody/ImmunoglobulinyesIntegrin_alpha, FG-GAP, Int_alpha_beta-p
ITGB4Antibody/ImmunoglobulinyesEGF, Integrin_bsu_VWA, Calx_beta
ITGA6-AS1Other/Unknownno
GALK1Kinaseyes2.7.1.6Galactokinase, GHMP_knse_ATP-bd_CS, GHMP_kinase_N_dom
MYO6Scaffold/PPInoMyosin_head_motor_dom-like, SH3_Myosin, Myosin_S1_N
PLECScaffold/PPInoPlectin_repeat, SH3_domain, Actinin_actin-bd_CS

Expression context

Cohort genes with no expression data: 0.

6 cohort genes are a single-cell marker in ≥1 SCXA experiment.

Breadth distribution (Bgee present_calls)

BucketGenes
narrow (1-5 tissues)0
moderate (6-20)0
broad (>20)6
unknown0

Top tissues across cohort

TissueCohort genes
tibial nerve3
sural nerve2
dorsal root ganglion1
minor salivary gland1
skin of leg1
bone marrow cell1
colonic epithelium1
male germ line stem cell (sensu Vertebrata) in testis1
apex of heart1
monocyte1
right lobe of liver1
amniotic fluid1
corpus callosum1
medial globus pallidus1
hindlimb stylopod muscle1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
ITGA6297ubiquitousmarkertibial nerve, sural nerve, dorsal root ganglion
ITGB4267broadmarkertibial nerve, minor salivary gland, skin of leg
ITGA6-AS1130markercolonic epithelium, male germ line stem cell (sensu Vertebrata) in testis, bone marrow cell
GALK1174ubiquitousmarkerright lobe of liver, apex of heart, monocyte
MYO6278ubiquitousmarkeramniotic fluid, medial globus pallidus, corpus callosum
PLEC283ubiquitousmarkersural nerve, hindlimb stylopod muscle, tibial nerve

Protein interactions among cohort

Intra-cohort edges: 3.

Hub genes (top 10 by interactor count)

SymbolInteractor count
PLEC3,529
ITGA63,130
MYO62,972
ITGB42,536
GALK12,244
ITGA6-AS10

Intra-cohort edges

ABSources
ITGA6ITGB4intact, string_interaction
ITGA6PLECstring_interaction
ITGB4PLECintact, string_interaction

Structural data

PDB: 5 · AlphaFold-only: 0 · No structure: 1

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
GALK1P5157020
PLECQ1514914
ITGB4P1614413
MYO6Q9UM548
ITGA6P232292

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 41. Enrichment computed across 6 evidence-associated genes (5 with Reactome annotation).

Pathways by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 5 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Type I hemidesmosome assembly3622.9×3e-07ITGA6, ITGB4, PLEC
Assembly of collagen fibrils and other multimeric structures3120.2×2e-05ITGA6, ITGB4, PLEC
Collagen formation2182.7×5e-04ITGA6, ITGB4
Syndecan interactions2169.2×5e-04ITGA6, ITGB4
Laminin interactions2152.3×5e-04ITGA6, ITGB4
Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin2111.4×9e-04ITGA6, ITGB4
Developmental Cell Lineages289.6×0.001ITGA6, ITGB4
Cell junction organization274.9×0.001ITGA6, ITGB4
Defective GALK1 causes GALCT212284.0×0.002GALK1
Non-integrin membrane-ECM interactions261.7×0.002ITGA6, ITGB4
Cell-Cell communication255.0×0.002ITGA6, ITGB4
Extracellular matrix organization225.2×0.008ITGA6, ITGB4
Galactose catabolism1326.3×0.010GALK1
Gap junction degradation1190.3×0.014MYO6
Caspase-mediated cleavage of cytoskeletal proteins1190.3×0.014PLEC
RHOBTB GTPase Cycle1163.1×0.015MYO6
Glutamate binding, activation of AMPA receptors and synaptic plasticity1152.3×0.015MYO6
Developmental Lineage of Mammary Stem Cells1152.3×0.015ITGA6
Developmental Lineage of Mammary Gland Alveolar Cells1126.9×0.017ITGA6
Trafficking of AMPA receptors1108.8×0.017MYO6
Developmental Lineage of Mammary Gland Myoepithelial Cells1108.8×0.017ITGA6
Gap junction trafficking and regulation195.2×0.017MYO6
Gap junction trafficking195.2×0.017MYO6
RHOBTB2 GTPase cycle195.2×0.017MYO6
RHOBTB1 GTPase cycle195.2×0.017MYO6
Developmental Lineage of Mammary Gland Luminal Epithelial Cells191.4×0.017ITGA6
Basigin interactions187.8×0.017ITGA6
RHOU GTPase cycle155.7×0.026MYO6
Integrin cell surface interactions126.9×0.052ITGA6
Developmental Biology25.8×0.057ITGA6, ITGB4

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 5 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
hemidesmosome assembly2963.0×5e-05ITGB4, PLEC
nail development2963.0×5e-05ITGA6, ITGB4
skin morphogenesis2561.7×1e-04ITGA6, ITGB4
galactitol metabolic process13370.4×0.003GALK1
protein-containing complex organization13370.4×0.003PLEC
glycolytic process from galactose13370.4×0.003GALK1
actomyosin contractile ring assembly actin filament organization13370.4×0.003PLEC
cell-matrix adhesion265.4×0.003ITGA6, ITGB4
integrin-mediated signaling pathway264.2×0.003ITGA6, ITGB4
skeletal myofibril assembly11685.2×0.004PLEC
leukocyte migration involved in immune response11123.5×0.004PLEC
peripheral nervous system myelin formation11123.5×0.004ITGB4
cellular response to hydrostatic pressure11123.5×0.004PLEC
intracellular protein localization241.9×0.004MYO6, PLEC
cell-cell adhesion240.6×0.004ITGA6, ITGB4
ectodermal cell differentiation1842.6×0.005ITGA6
beta-D-galactose catabolic process via UDP-galactose, Leloir pathway1674.1×0.006GALK1
tight junction organization1674.1×0.006PLEC
cell-substrate junction assembly1561.7×0.006ITGA6
regulation of secretion1561.7×0.006MYO6
trophoblast cell migration1481.5×0.007ITGB4
galactose metabolic process1421.3×0.008GALK1
keratinocyte development1306.4×0.009PLEC
peripheral nervous system myelin maintenance1306.4×0.009PLEC
mesodermal cell differentiation1306.4×0.009ITGB4
cellular response to fluid shear stress1259.3×0.011PLEC
inner ear auditory receptor cell differentiation1240.7×0.011MYO6
T cell chemotaxis1224.7×0.011PLEC
regulation of vascular permeability1224.7×0.011PLEC
intermediate filament cytoskeleton organization1187.2×0.013PLEC

Therapeutics

Drug target analysis

Approved (phase 4): 1 · Phase ≥3: 1 · Phased (≥1): 1 · Undrugged: 5

Druggability breadth: 4 of 6 evidence-associated genes (67%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Genes with an approved drug

The molecule shown is one approved compound that hits the gene — not necessarily a drug of choice or one indicated for this disease.

SymbolExample approved molecule
GALK1PYRANTEL PAMOATE

Top cohort targets by molecule count

SymbolMoleculesMax phase
GALK164
ITGA600
ITGB400
ITGA6-AS100
MYO600
PLEC00

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
PYRANTEL PAMOATE4GALK1
HEXACHLOROPHENE4GALK1
QUERCETIN3GALK1
GOSSYPOL3GALK1
STREPTONIGRIN2GALK1
LUTEOLIN2GALK1

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

Cohort genes with ChEMBL bioactivity (full, sorted by assay count)

SymbolAssaysType breakdown
GALK119Binding:15, Functional:4
PLEC12Binding:12
ITGA63Binding:3
ITGB42Binding:2

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
GALK12.7.1.6galactokinase

Pharmacogenomics

Cohort genes with a PharmGKB record: 5; with CPIC/DPWG dosing guidelines: 0.

No cohort gene has a CPIC/DPWG genotype-guided dosing guideline (PharmGKB).

Chemical tractability of cohort targets

6 approved/phased compounds have measured bioactivity against a cohort gene (and aren’t yet in disease-level trials). This is a research / tractability signal, NOT a therapeutic recommendation — a bioactivity row often reflects off-target or screening binding (e.g. promiscuous kinase inhibitors against a cohort kinase), implying no disease mechanism.

CompoundMax phaseCohort target (bioactivity)
PYRANTEL PAMOATE4GALK1
HEXACHLOROPHENE4GALK1
QUERCETIN3GALK1
GOSSYPOL3GALK1
STREPTONIGRIN2GALK1
LUTEOLIN2GALK1

Druggability pyramid

Cohort genes binned by druggability tier (high → low):

TierDefinitionGenesSymbols
AApproved (phase 4 drug)1GALK1
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug2ITGA6, ITGB4
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug3ITGA6-AS1, MYO6, PLEC

Undrugged target profiles

5 cohort genes are undrugged. Ranked by ‘starting-point quality’ (assay depth + drugged-partner adjacency).

SymbolChEMBL assaysDrugged partners (top 3)
ITGA63
ITGB42
ITGA6-AS10
MYO60
PLEC12

Clinical trials & evidence

Clinical trials

Clinical trials: 0.