X-linked Alport syndrome

disease
On this page

Also known as Alport syndrome 1, X-linked, X-linked dominantAlport syndrome, X-linkedATScongenital hereditary hematuriahemorrhagic familial nephritishemorrhagic hereditary nephritisnephropathy and deafness, X-linked

Summary

X-linked Alport syndrome (MONDO:0010520) is a disease caused by COL4A5 (GenCC Definitive), with 6 cohort genes and 3 clinical trials. The dominant Reactome pathway is Fibronectin matrix formation (3 cohort genes). Top therapeutic interventions include benazepril, hydroxychloroquine, and elx-02.

At a glance

  • Prevalence: 1-9 / 100 000 (Sweden) [Orphanet-validated]
  • Causal gene: COL4A5 (GenCC Definitive)
  • Cohort genes: 6
  • ClinVar variants: 1,310
  • Clinical trials: 3

Clinical features

Epidemiology

Prevalence records

2 prevalence record(s), Orphanet:

TypeClassValueGeographyValidation
Prevalence at birth1-9 / 100 0001.25SwedenValidated
Point prevalence1-9 / 100 000EuropeNot yet validated

Identifiers

Disease identifiers

FieldValue
Canonical nameX-linked Alport syndrome
Mondo IDMONDO:0010520
OMIM301050
Orphanet88917
DOIDDOID:0110034
SNOMED CT717768004
UMLSC4746986
MedGen1648433
GARD0016774
MedDRA10001843
Is cancer (heuristic)no

Also known as: Alport syndrome 1, X-linked, X-linked dominant · Alport syndrome, X-linked · ATS · congenital hereditary hematuria · hemorrhagic familial nephritis · hemorrhagic hereditary nephritis · nephropathy and deafness, X-linked · X-linked Alport syndrome

Data availability: 1,310 ClinVar variants · 4 GenCC gene-disease records.

Disease family

Classification path: disease › human disease › disease by etiologic mechanism › disease of genetic or genomic mechanism › hereditary diseaseX-linked diseaseX-linked Alport syndrome

Related subtypes (49): X-linked Opitz G/BBB syndrome, X-linked immunoneurologic disorder, X-linked adrenal hypoplasia congenita, X-linked lissencephaly with abnormal genitalia, X-linked severe congenital neutropenia, X-linked distal spinal muscular atrophy type 3, epilepsy, X-linked 1, with variable learning disabilities and behavior disorders, Aland island eye disease, X-linked erythropoietic protoporphyria, X-linked central congenital hypothyroidism with late-onset testicular enlargement, X-linked colobomatous microphthalmia-microcephaly-intellectual disability-short stature syndrome, X-linked acrogigantism due to Xq26 microduplication, Wiskott-Aldrich syndrome, X-linked mandibulofacial dysostosis, X-linked chondrodysplasia punctata, choroideremia, cone dystrophy, X-linked, with tapetal-like sheen, diabetes insipidus, nephrogenic, X-linked, Dyggve-Melchior-Clausen syndrome, X-linked, dyskeratosis congenita, X-linked, X-linked hypohidrotic ectodermal dysplasia, X-linked Ehlers-Danlos syndrome, epidermodysplasia verruciformis, X-linked, exudative vitreoretinopathy 2, X-linked, Aarskog-Scott syndrome, X-linked, hemophilia A, X-linked hydrocephalus with stenosis of the aqueduct of Sylvius, hyper-IgM syndrome type 1, X-linked lymphoproliferative syndrome, macular dystrophy, X-linked, X-linked Emery-Dreifuss muscular dystrophy, X-linked myotubular myopathy, X-linked lethal multiple pterygium syndrome, X-linked retinoschisis, spondyloepiphyseal dysplasia tarda, X-linked, X-linked cerebellar ataxia, adrenoleukodystrophy, Charcot-Marie-Tooth disease type X, X-linked dominant disease, X-linked recessive disease, X-linked hypophosphatemic rickets, X-linked sideroblastic anemia 1, X-linked deafness, X-linked cone-rod dystrophy, X-linked congenital stationary night blindness, X-linked congenital hemolytic anemia, X-linked complex neurodevelopmental disorder, X-linked intellectual disability, leukemia, acute, X-linked

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:

178 likely pathogenic, 138 pathogenic, 86 pathogenic/likely pathogenic, 75 uncertain significance, 55 conflicting classifications of pathogenicity, 28 likely benign, 21 benign, 19 benign/likely benign

ClinVarVariant (HGVS)GeneClassificationReview
10460Multiple allelesPathogenicno assertion criteria provided
10464NM_033380.2(COL4A5):c.[866G>T;4282C>T]Pathogenicno assertion criteria provided
10453NG_011977.2:g.(239831_242576)_(252772_257824)delCOL4A5Pathogenicno assertion criteria provided
10455COL4A5, 10-15-KB INS, 40-KB DELCOL4A5Pathogenicno assertion criteria provided
10456NG_011977.2:g.(246966_251107)_?delCOL4A5Pathogenicno assertion criteria provided
10457NG_011977.2:g.?_(146097_162513)delCOL4A5Pathogenicno assertion criteria provided
10458NM_033380.3(COL4A5):c.3428G>A (p.Gly1143Asp)COL4A5Pathogeniccriteria provided, single submitter
10462NM_033380.3(COL4A5):c.1561G>T (p.Gly521Cys)COL4A5Pathogenicno assertion criteria provided
10463NM_033380.3(COL4A5):c.974G>A (p.Gly325Glu)COL4A5Pathogenicno assertion criteria provided
10465NM_033380.3(COL4A5):c.161G>A (p.Gly54Asp)COL4A5Pathogenicno assertion criteria provided
10466NM_033380.3(COL4A5):c.4964T>G (p.Leu1655Arg)COL4A5Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
10467NM_033380.3(COL4A5):c.5048G>A (p.Arg1683Gln)COL4A5Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1066338NM_033380.3(COL4A5):c.2998G>A (p.Gly1000Arg)COL4A5Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1066653NM_033380.3(COL4A5):c.2042-2A>GCOL4A5Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1066732NM_033380.3(COL4A5):c.3347G>A (p.Gly1116Glu)COL4A5Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1066759NM_033380.3(COL4A5):c.3107G>A (p.Gly1036Glu)COL4A5Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1067067NM_033380.3(COL4A5):c.1370G>A (p.Gly457Asp)COL4A5Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1068943NM_033380.3(COL4A5):c.4528+2T>CCOL4A5Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1072946NM_033380.3(COL4A5):c.1862G>A (p.Gly621Asp)COL4A5Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1073265NM_033380.3(COL4A5):c.4706+2T>CCOL4A5Pathogeniccriteria provided, multiple submitters, no conflicts
1073893NM_033380.3(COL4A5):c.4706+1G>TCOL4A5Pathogeniccriteria provided, multiple submitters, no conflicts
1075985NM_033380.3(COL4A5):c.3584dup (p.Gly1196fs)COL4A5Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1076557NM_033380.3(COL4A5):c.874G>A (p.Gly292Arg)COL4A5Pathogeniccriteria provided, multiple submitters, no conflicts
1076952NM_033380.3(COL4A5):c.1808G>A (p.Gly603Asp)COL4A5Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1077037NM_033380.3(COL4A5):c.439-1G>ACOL4A5Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1077042NM_033380.3(COL4A5):c.4978_4979insAAAA (p.Val1660fs)COL4A5Pathogeniccriteria provided, single submitter
1077043NM_033380.3(COL4A5):c.1871G>T (p.Gly624Val)COL4A5Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1077046NM_033380.3(COL4A5):c.2146G>A (p.Gly716Ser)COL4A5Pathogeniccriteria provided, single submitter
1077047NM_033380.3(COL4A5):c.1033-2A>GCOL4A5Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1077050NM_033380.3(COL4A5):c.1480G>T (p.Gly494Cys)COL4A5Pathogeniccriteria provided, single submitter

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 6 · Orphanet: 9 · 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
COL4A5DefinitiveX-linkedAlport syndrome6

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
COL4A5Orphanet:1018X-linked Alport syndrome-diffuse leiomyomatosis
COL4A5Orphanet:653722Digenic Alport syndrome
COL4A5Orphanet:88917X-linked Alport syndrome
COL4A4Orphanet:653722Digenic Alport syndrome
COL4A4Orphanet:88918Autosomal dominant Alport syndrome
COL4A4Orphanet:88919Autosomal recessive Alport syndrome
FN1Orphanet:84090Fibronectin glomerulopathy
FN1Orphanet:93315Spondylometaphyseal dysplasia, ‘corner fracture’ type
MSR1Orphanet:1331Familial prostate cancer

Cohort genes → proteins

6 cohort genes, 6 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence6

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
COL4A5HGNC:2207ENSG00000188153P29400Collagen alpha-5(IV) chaingencc,clinvar
ATG4AHGNC:16489ENSG00000101844Q8WYN0Cysteine protease ATG4Aclinvar
COL4A4HGNC:2206ENSG00000081052P53420Collagen alpha-4(IV) chainclinvar
ZC3H12CHGNC:29362ENSG00000149289Q9C0D7Probable ribonuclease ZC3H12Cclinvar
FN1HGNC:3778ENSG00000115414P02751Fibronectinclinvar
MSR1HGNC:7376ENSG00000038945P21757Macrophage scavenger receptor types I and IIclinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
COL4A5Collagen alpha-5(IV) chainType IV collagen is the major structural component of glomerular basement membranes (GBM), forming a ‘chicken-wire’ meshwork together with laminins, proteoglycans and entactin/nidogen.
ATG4ACysteine protease ATG4ACysteine protease that plays a key role in autophagy by mediating both proteolytic activation and delipidation of ATG8 family proteins.
COL4A4Collagen alpha-4(IV) chainType IV collagen is the major structural component of glomerular basement membranes (GBM), forming a ‘chicken-wire’ meshwork together with laminins, proteoglycans and entactin/nidogen.
ZC3H12CProbable ribonuclease ZC3H12CMay function as RNase and regulate the levels of target RNA species.
FN1FibronectinFibronectins bind cell surfaces and various compounds including collagen, fibrin, heparin, DNA, and actin.
MSR1Macrophage scavenger receptor types I and IIMembrane glycoproteins implicated in the pathologic deposition of cholesterol in arterial walls during atherogenesis.

Protein-family classification

Druggable: 2 · Difficult: 1 · Unknown: 3 · Druggable fraction: 0.33

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
Protease16.1×0.377
Antibody/Immunoglobulin14.9×0.377
Transcription factor11.4×0.719
Other/Unknown30.9×0.758

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
COL4A5Other/UnknownnoCollagen_IV_NC, Collagen, CTDL_fold
ATG4AProteaseyesPeptidase_C54, Papain-like_cys_pep_sf, Peptidase_C54_cat
COL4A4Other/UnknownnoCollagen_IV_NC, Collagen, CTDL_fold
ZC3H12CTranscription factornoZnf_CCCH, RNase_Zc3h12_NYN, Rege-1_UBA-like
FN1Antibody/ImmunoglobulinyesFibronectin_type1, FN_type2_dom, FN3_dom
MSR1Other/UnknownnoSRCR, SR-AI/II, Collagen

Expression context

Cohort genes with no expression data: 0.

5 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
lower esophagus muscularis layer1
mucosa of stomach1
ventricular zone1
body of pancreas1
gastrocnemius1
hindlimb stylopod muscle1
metanephros cortex1
pigmented layer of retina1
renal medulla1
biceps brachii1
epithelial cell of pancreas1
tibialis anterior1
decidua1
right coronary artery1
synovial joint1
right lung1
upper lobe of left lung1
upper lobe of lung1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
COL4A5267ubiquitousmarkermucosa of stomach, ventricular zone, lower esophagus muscularis layer
ATG4A272ubiquitousmarkerbody of pancreas, gastrocnemius, hindlimb stylopod muscle
COL4A4187broadmarkerrenal medulla, metanephros cortex, pigmented layer of retina
ZC3H12C247ubiquitousyestibialis anterior, epithelial cell of pancreas, biceps brachii
FN1292ubiquitousmarkersynovial joint, right coronary artery, decidua
MSR1206broadmarkerright lung, upper lobe of left lung, upper lobe of lung

Protein interactions among cohort

Intra-cohort edges: 1.

Hub genes (top 10 by interactor count)

SymbolInteractor count
FN18,860
MSR12,259
COL4A51,738
COL4A41,243
ATG4A1,161
ZC3H12C570

Intra-cohort edges

ABSources
COL4A4COL4A5string_interaction

Structural data

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

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
FN1P0275165
COL4A5P294002
COL4A4P534202
ATG4AQ8WYN01
MSR1P217571

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
ZC3H12CQ9C0D758.15

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 44. 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
Fibronectin matrix formation3342.6×2e-06COL4A5, COL4A4, FN1
Attachment of bacteria to epithelial cells3297.9×2e-06COL4A5, COL4A4, FN1
Non-integrin membrane-ECM interactions392.6×3e-05COL4A5, COL4A4, FN1
ECM proteoglycans390.2×3e-05COL4A5, COL4A4, FN1
Integrin cell surface interactions380.6×3e-05COL4A5, COL4A4, FN1
Anchoring fibril formation2304.5×1e-04COL4A5, COL4A4
Crosslinking of collagen fibrils2228.4×2e-04COL4A5, COL4A4
Laminin interactions2152.3×4e-04COL4A5, COL4A4
Collagen chain trimerization2103.8×6e-04COL4A5, COL4A4
Signaling by PDGF2101.5×6e-04COL4A5, COL4A4
NCAM1 interactions299.3×6e-04COL4A5, COL4A4
Assembly of collagen fibrils and other multimeric structures280.1×9e-04COL4A5, COL4A4
Collagen degradation270.3×0.001COL4A5, COL4A4
Collagen biosynthesis and modifying enzymes268.2×0.001COL4A5, COL4A4
ALK mutants bind TKIs1190.3×0.015FN1
p130Cas linkage to MAPK signaling for integrins1152.3×0.018FN1
GRB2:SOS provides linkage to MAPK signaling for Integrins1142.8×0.018FN1
Scavenging by Class A Receptors1120.2×0.020MSR1
Binding and Uptake of Ligands by Scavenger Receptors1108.8×0.021MSR1
Syndecan interactions184.6×0.025FN1
Integrin signaling184.6×0.025FN1
MET activates PTK2 signaling176.1×0.026FN1
Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells171.4×0.027FN1
Signaling by high-kinase activity BRAF mutants163.4×0.028FN1
Molecules associated with elastic fibres161.7×0.028FN1
MAP2K and MAPK activation157.1×0.028FN1
Signaling by RAF1 mutants155.7×0.028FN1
Signaling by moderate kinase activity BRAF mutants150.8×0.028FN1
Paradoxical activation of RAF signaling by kinase inactive BRAF150.8×0.028FN1
Signaling downstream of RAS mutants150.8×0.028FN1

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
negative regulation of monocyte activation11123.5×0.010FN1
calcium-independent cell-matrix adhesion1842.6×0.010FN1
plasma lipoprotein particle clearance1842.6×0.010MSR1
positive regulation of substrate-dependent cell migration, cell attachment to substrate1842.6×0.010FN1
protein delipidation1674.1×0.010ATG4A
negative regulation of transforming growth factor beta production1674.1×0.010FN1
cell-substrate junction assembly1561.7×0.010FN1
biological process involved in interaction with symbiont1561.7×0.010FN1
collagen fibril organization289.9×0.010COL4A5, COL4A4
autophagy244.1×0.010ATG4A, FN1
positive regulation of cholesterol storage1481.5×0.011MSR1
neural crest cell migration involved in autonomic nervous system development1374.5×0.012FN1
aggrephagy1337.0×0.012ATG4A
blood coagulation, fibrin clot formation1337.0×0.012FN1
glomerular basement membrane development1306.4×0.012COL4A4
integrin activation1280.9×0.012FN1
collagen-activated tyrosine kinase receptor signaling pathway1259.3×0.013COL4A5
regulation of protein phosphorylation1224.7×0.014FN1
lipoprotein transport1198.3×0.014MSR1
enteric nervous system development1198.3×0.014FN1
piecemeal microautophagy of the nucleus1187.2×0.014ATG4A
amyloid-beta clearance1187.2×0.014MSR1
positive regulation of macrophage derived foam cell differentiation1168.5×0.014MSR1
cholesterol transport1146.5×0.016MSR1
phagocytosis, engulfment1134.8×0.017MSR1
response to muscle activity1116.2×0.018FN1
regulation of ERK1 and ERK2 cascade1116.2×0.018FN1
neuromuscular junction development1105.3×0.019COL4A5
positive regulation of axon extension1102.1×0.019FN1
endodermal cell differentiation199.1×0.019FN1

Therapeutics

Drug target analysis

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

Druggability breadth: 5 of 6 evidence-associated genes (83%) 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
ATG4ATIOCONAZOLE

Top cohort targets by molecule count

SymbolMoleculesMax phase
ATG4A14
COL4A500
COL4A400
ZC3H12C00
FN100
MSR100

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
TIOCONAZOLE4ATG4A

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

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

SymbolAssaysType breakdown
ATG4A1Binding:1
FN11Binding:1
MSR11Binding:1

Pharmacogenomics

Cohort genes with a PharmGKB record: 6; with CPIC/DPWG dosing guidelines: 0.

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

Chemical tractability of cohort targets

1 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)
TIOCONAZOLE4ATG4A

Druggability pyramid

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

TierDefinitionGenesSymbols
AApproved (phase 4 drug)1ATG4A
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug1FN1
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug4COL4A5, COL4A4, ZC3H12C, MSR1

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
COL4A50
COL4A40
ZC3H12C0
FN11
MSR11

Clinical trials & evidence

Clinical trials

Clinical trials: 3.

Phase distribution (across all retrieved trials)

PhaseTrials
PHASE22
Not specified1

Top trials by phase / activity

NCTPhaseStatusTitle
NCT07523581PHASE2NOT_YET_RECRUITINGEXACT Study: A Blinded Study in Patients With Alport Syndrome to Evaluate Exaluren Efficacy and Safety
NCT04937907PHASE2COMPLETEDStudy of Hydroxychloroquine in Patients With X-linked Alport Syndrome in China (CHXLAS)
NCT03655223Not specifiedENROLLING_BY_INVITATIONEarly Check: Expanded Screening in Newborns

Drugs tested across these trials (top 30)

MoleculeMax phaseTrials referencing
BENAZEPRIL41
HYDROXYCHLOROQUINE41
ELX-0221