Systemic primary carnitine deficiency disease

disease
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Also known as Carnitine deficiencyCARNITINE deficiency, systemic primaryCarnitine deficiency, systemic, due to defect in renal reabsorption of carnitineCarnitine plasma-membrane transporter deficiencyCarnitine transporter defectcarnitine transporter deficiencycarnitine uptake defectCarnitine uptake deficiencyCDSPCUDdeficiency of plasma-membrane carnitine transporterprimary carnitine deficiencyrenal carnitine transport defectSPCD

Summary

Systemic primary carnitine deficiency disease (MONDO:0008919) is a disease caused by SLC22A5 (GenCC Definitive), with 7 cohort genes and 6 clinical trials. Top therapeutic interventions include levocarnitine, carnitine, and dextrocarnitine.

At a glance

  • Prevalence: 6-9 / 10 000 (Faroe Islands) [Orphanet-validated]
  • Causal gene: SLC22A5 (GenCC Definitive)
  • Cohort genes: 7
  • ClinVar variants: 1,231
  • Phenotypes (HPO): 9
  • Clinical trials: 6

Clinical features

Epidemiology

Prevalence records

7 prevalence record(s), Orphanet:

TypeClassValueGeographyValidation
Prevalence at birth1-9 / 100 0003.2EuropeValidated
Annual incidence>1 / 1000138.9Faroe IslandsValidated
Point prevalence6-9 / 10 00077Faroe IslandsValidated
Point prevalence<1 / 1 000 0000.0069ChinaValidated
Prevalence at birth1-9 / 100 0003.2United StatesValidated
Prevalence at birth1-9 / 100 0002.5JapanValidated
Prevalence at birth1-9 / 1 000 0000.83AustraliaValidated

Signs & symptoms

Clinical features (HPO)

9 HPO clinical features (Orphanet curated; top 9 by frequency):

HPO IDTermFrequency
HP:0000467Neck muscle weaknessVery frequent (80-99%)
HP:0001289ConfusionVery frequent (80-99%)
HP:0001324Muscle weaknessVery frequent (80-99%)
HP:0002013VomitingVery frequent (80-99%)
HP:0002240HepatomegalyVery frequent (80-99%)
HP:0002312ClumsinessVery frequent (80-99%)
HP:0002910Elevated circulating hepatic transaminase concentrationVery frequent (80-99%)
HP:0006846Acute encephalopathyVery frequent (80-99%)
HP:0007334Bilateral tonic-clonic seizure with focal onsetVery frequent (80-99%)

Identifiers

Disease identifiers

FieldValue
Canonical namesystemic primary carnitine deficiency disease
Mondo IDMONDO:0008919
MeSHC536778
OMIM212140
Orphanet158
DOIDDOID:14365
ICD-10-CME71.41
NCITC98864
SNOMED CT21764004
UMLSC0342788
MedGen90999
GARD0005104
Is cancer (heuristic)no

Also known as: Carnitine deficiency · CARNITINE deficiency, systemic primary · Carnitine deficiency, systemic, due to defect in renal reabsorption of carnitine · Carnitine plasma-membrane transporter deficiency · Carnitine transporter defect · carnitine transporter deficiency · carnitine uptake defect · Carnitine uptake deficiency · CDSP · CUD · cud · deficiency of plasma-membrane carnitine transporter · primary carnitine deficiency · renal carnitine transport defect · SPCD · systemic primary carnitine deficiency disease

Data availability: 1,231 ClinVar variants · 7 GenCC gene-disease records · 2 cell lines.

Disease family

Classification path: disease › human disease › disease by etiologic mechanism › disease of genetic or genomic mechanism › hereditary diseaseinborn errors of metabolism › inborn disorder of amino acid and other organic acid metabolism › inborn disorder of amino acid metabolismsystemic primary carnitine deficiency disease

Related subtypes (32): disorder of methionine catabolism, inborn serine deficiency, cerebral creatine deficiency syndrome, inborn organic aciduria, gamma-amino butyric acid metabolism disorder, homocystinuria, urea cycle disorder, adenylosuccinate lyase deficiency, cystathioninuria, hyperlysinemia, Brunner syndrome, glycine encephalopathy, aminoacylase 1 deficiency, adenine phosphoribosyltransferase deficiency, hyperphenylalaninemia due to tetrahydrobiopterin deficiency, inborn disorder of tryptophan metabolism, inborn disorder of proline metabolism, inborn disorder of ornithine metabolism, inborn disorder of amino acid transport, inborn disorder of histidine metabolism, inborn disorder of phenylalanine and tyrosine metabolism, inborn disorder of branched-chain amino acid metabolism, arakawa syndrome 2, 2-methylacetoacetyl CoA thiolase deficiency, albinism, hyperphenylalaninemia due to DNAJC12 deficiency, inborn disorder of the metabolism of sulfur-containing amino acids and hydrogen sulfide, inborn disorder of glycine and serine metabolism, inborn disorder of ornithine, proline and hydroxyproline metabolism, inborn disorder of glutamate/glutamine and aspartate/asparagine metabolism, hyperglycinemia, transient neonatal, tetrahydrobiopterin (BH4)-deficient hyperphenylalaninemia

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:

229 likely benign, 197 uncertain significance, 49 pathogenic, 41 conflicting classifications of pathogenicity, 41 pathogenic/likely pathogenic, 30 likely pathogenic, 10 benign, 3 benign/likely benign

ClinVarVariant (HGVS)GeneClassificationReview
1206321NM_020812.4(DOCK6):c.3190_3191del (p.Leu1064fs)DOCK6Pathogeniccriteria provided, multiple submitters, no conflicts
25340NM_003060.4(SLC22A5):c.-149G>ALOC129994569Pathogeniccriteria provided, multiple submitters, no conflicts
1042938NM_003060.4(SLC22A5):c.113C>A (p.Ser38Tyr)SLC22A5Pathogeniccriteria provided, single submitter
1068475NM_003060.4(SLC22A5):c.1520T>C (p.Leu507Ser)SLC22A5Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1068602NC_000005.9:g.(?131713846)(131714183_?)delSLC22A5Pathogeniccriteria provided, single submitter
1068603NC_000005.9:g.(?131719829)(131728317_?)delSLC22A5Pathogeniccriteria provided, single submitter
1068932NM_003060.4(SLC22A5):c.37G>T (p.Glu13Ter)SLC22A5Pathogeniccriteria provided, single submitter
1069784NM_003060.4(SLC22A5):c.1240del (p.Leu414fs)SLC22A5Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1070131NM_003060.4(SLC22A5):c.587_588del (p.Phe196fs)SLC22A5Pathogeniccriteria provided, single submitter
1070906NM_003060.4(SLC22A5):c.844dup (p.Arg282fs)SLC22A5Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1071451NM_003060.4(SLC22A5):c.2T>C (p.Met1Thr)SLC22A5Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1072441NM_003060.4(SLC22A5):c.1347C>A (p.Tyr449Ter)SLC22A5Pathogeniccriteria provided, single submitter
1074182NM_003060.4(SLC22A5):c.479C>A (p.Ser160Ter)SLC22A5Pathogeniccriteria provided, single submitter
1367433NM_003060.4(SLC22A5):c.1350del (p.Ala451fs)SLC22A5Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1398476NM_003060.4(SLC22A5):c.860_861del (p.Gln287fs)SLC22A5Pathogeniccriteria provided, single submitter
1417216NM_003060.4(SLC22A5):c.328C>T (p.Gln110Ter)SLC22A5Pathogeniccriteria provided, single submitter
1419604NM_003060.4(SLC22A5):c.1446C>G (p.Tyr482Ter)SLC22A5Pathogeniccriteria provided, single submitter
1424747NM_003060.4(SLC22A5):c.847T>C (p.Trp283Arg)SLC22A5Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1424767NM_003060.4(SLC22A5):c.1336G>T (p.Val446Phe)SLC22A5Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1426461NM_003060.4(SLC22A5):c.976C>T (p.Gln326Ter)SLC22A5Pathogeniccriteria provided, single submitter
1430105NM_003060.4(SLC22A5):c.69_71del (p.Phe23del)SLC22A5Pathogeniccriteria provided, single submitter
1432590NM_003060.4(SLC22A5):c.835G>T (p.Glu279Ter)SLC22A5Pathogeniccriteria provided, single submitter
1451189NM_003060.4(SLC22A5):c.859C>T (p.Gln287Ter)SLC22A5Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1451545NM_003060.4(SLC22A5):c.839C>T (p.Ser280Phe)SLC22A5Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1451891NM_003060.4(SLC22A5):c.802del (p.Val268fs)SLC22A5Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1452650NM_003060.4(SLC22A5):c.1289del (p.Val430fs)SLC22A5Pathogeniccriteria provided, single submitter
1453057NM_003060.4(SLC22A5):c.449del (p.Phe150fs)SLC22A5Pathogeniccriteria provided, single submitter
1453608NM_003060.4(SLC22A5):c.494_497del (p.Asp165fs)SLC22A5Pathogeniccriteria provided, single submitter
1455669NC_000005.9:g.(?131713846)(131720003_?)delSLC22A5Pathogeniccriteria provided, single submitter
1456659NM_003060.4(SLC22A5):c.1412G>C (p.Arg471Pro)SLC22A5Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 9 · Orphanet: 3 · 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
SLC22A5DefinitiveAutosomal recessivesystemic primary carnitine deficiency disease9

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
SLC22A5Orphanet:158Systemic primary carnitine deficiency
ZBTB18Orphanet:36367Distal deletion 1q syndrome
DOCK6Orphanet:974Adams-Oliver syndrome

Cohort genes → proteins

7 cohort genes, 6 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence7

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
SLC22A5HGNC:10969ENSG00000197375O76082Organic cation/carnitine transporter 2gencc,clinvar
SLC22A4HGNC:10968ENSG00000197208Q9H015Solute carrier family 22 member 4clinvar
ZBTB18HGNC:13030ENSG00000179456Q99592Zinc finger and BTB domain-containing protein 18clinvar
ACSL6HGNC:16496ENSG00000164398Q9UKU0Long-chain-fatty-acid–CoA ligase 6clinvar
DOCK6HGNC:19189ENSG00000130158Q96HP0Dedicator of cytokinesis protein 6clinvar
RNF167HGNC:24544ENSG00000108523Q9H6Y7E3 ubiquitin-protein ligase RNF167clinvar
MIR3936HGHGNC:40538ENSG00000233006MIR3936 host geneclinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
SLC22A5Organic cation/carnitine transporter 2Sodium-ion dependent, high affinity carnitine transporter.
SLC22A4Solute carrier family 22 member 4Transporter that mediates the transport of endogenous and microbial zwitterions and organic cations.
ZBTB18Zinc finger and BTB domain-containing protein 18Transcriptional repressor that plays a role in various developmental processes such as myogenesis and brain development.
ACSL6Long-chain-fatty-acid–CoA ligase 6Catalyzes the conversion of long-chain fatty acids to their active form acyl-CoA for both synthesis of cellular lipids, and degradation via beta-oxidation.
DOCK6Dedicator of cytokinesis protein 6Acts as a guanine nucleotide exchange factor (GEF) for CDC42 and RAC1 small GTPases.
RNF167E3 ubiquitin-protein ligase RNF167E3 ubiquitin-protein ligase that acts as a regulator of the TORC1 signaling pathway.

Protein-family classification

Druggable: 3 · Difficult: 2 · Unknown: 2 · Druggable fraction: 0.43

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
Transporter222.2×0.013
Transcription factor22.4×0.408
Enzyme (other)11.7×0.609
Other/Unknown20.5×0.968

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
SLC22A5TransporteryesOrgcat_transp/SVOP, MFS_sugar_transport-like, Sugar_transporter_CS
SLC22A4TransporteryesOrgcat_transp/SVOP, MFS_sugar_transport-like, Sugar_transporter_CS
ZBTB18Transcription factornoBTB/POZ_dom, SKP1/BTB/POZ_sf, Znf_C2H2_type
ACSL6Enzyme (other)yes6.2.1.3AMP-dep_synth/lig_dom, AMP-binding_CS, ANL_N_sf
DOCK6Other/UnknownnoDOCK_C/D_N, DOCK, C2_DOCK-type_domain
RNF167Transcription factornoZnf_RING, PA_domain, Znf_RING-CH
MIR3936HGOther/Unknownno

Expression context

Cohort genes with no expression data: 0.

7 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)7
unknown0

Top tissues across cohort

TissueCohort genes
mucosa of transverse colon2
apex of heart2
gastrocnemius1
muscle of leg1
bronchial epithelial cell1
bronchus1
epithelium of bronchus1
cerebellar vermis1
cortical plate1
paraflocculus1
Brodmann (1909) area 231
lateral nuclear group of thalamus1
primary visual cortex1
colonic epithelium1
right lung1
granulocyte1
adenohypophysis1
metanephros cortex1
right uterine tube1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
SLC22A5235ubiquitousmarkergastrocnemius, mucosa of transverse colon, muscle of leg
SLC22A4201ubiquitousmarkerbronchial epithelial cell, epithelium of bronchus, bronchus
ZBTB18292ubiquitousmarkercerebellar vermis, paraflocculus, cortical plate
ACSL6210broadmarkerlateral nuclear group of thalamus, Brodmann (1909) area 23, primary visual cortex
DOCK6254ubiquitousmarkercolonic epithelium, right lung, apex of heart
RNF167288ubiquitousmarkergranulocyte, apex of heart, mucosa of transverse colon
MIR3936HG169broadmarkermetanephros cortex, adenohypophysis, right uterine tube

Protein interactions among cohort

Intra-cohort edges: 1.

Hub genes (top 10 by interactor count)

SymbolInteractor count
ACSL62,236
SLC22A41,615
ZBTB181,520
SLC22A51,492
DOCK61,018
RNF167791
MIR3936HG0

Intra-cohort edges

ABSources
SLC22A4SLC22A5intact

Structural data

PDB: 3 · AlphaFold-only: 3 · No structure: 1

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
DOCK6Q96HP07
SLC22A5O760823
ZBTB18Q995921

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
ACSL6Q9UKU090.15
SLC22A4Q9H01585.07
RNF167Q9H6Y779.08

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 19. Enrichment computed across 7 evidence-associated genes (4 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 4 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
SLC-mediated transport of organic cations2380.7×9e-05SLC22A5, SLC22A4
R-HSA-5491322380.7×9e-05SLC22A5, SLC22A4
R-HSA-425366290.6×0.001SLC22A5, SLC22A4
Fatty acid metabolism265.6×0.002SLC22A5, ACSL6
Defective SLC22A5 causes systemic primary carnitine deficiency (CDSP)11427.5×0.003SLC22A5
SLC-mediated transmembrane transport229.6×0.005SLC22A5, SLC22A4
Choline catabolism1356.9×0.008SLC22A4
Carnitine shuttle1190.3×0.012SLC22A5
Metabolism of lipids215.8×0.012SLC22A5, ACSL6
Synthesis of very long-chain fatty acyl-CoAs1114.2×0.014ACSL6
Fatty acyl-CoA biosynthesis1109.8×0.014ACSL6
Transport of small molecules212.6×0.014SLC22A5, SLC22A4
SLC transporter disorders151.0×0.028SLC22A5
Disorders of transmembrane transporters134.8×0.039SLC22A5
Metabolism25.8×0.050SLC22A5, ACSL6
CDC42 GTPase cycle118.1×0.064DOCK6
Factors involved in megakaryocyte development and platelet production116.6×0.066DOCK6
RAC1 GTPase cycle115.3×0.067DOCK6
Disease13.3×0.273SLC22A5

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 6 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
carnitine transport21404.3×2e-05SLC22A5, SLC22A4
quaternary ammonium group transport21123.5×2e-05SLC22A5, SLC22A4
sodium ion transport290.6×0.003SLC22A5, SLC22A4
sulfur amino acid transport12808.7×0.004SLC22A4
acetylcholine uptake11404.3×0.004SLC22A4
positive regulation of intestinal epithelial structure maintenance11404.3×0.004SLC22A5
sodium-dependent organic cation transport11404.3×0.004SLC22A5
(R)-carnitine transport11404.3×0.004SLC22A5
(R)-carnitine transmembrane transport1936.2×0.006SLC22A5
organelle localization1702.2×0.007RNF167
response to symbiotic bacterium1468.1×0.008SLC22A5
carnitine transmembrane transport1468.1×0.008SLC22A5
carnitine metabolic process1401.2×0.009SLC22A4
protein K29-linked ubiquitination1255.3×0.013RNF167
cellular response to leucine starvation1234.1×0.013RNF167
xenobiotic detoxification by transmembrane export across the plasma membrane1187.2×0.016SLC22A5
amino acid import across plasma membrane1175.5×0.016SLC22A4
long-chain fatty-acyl-CoA biosynthetic process1140.4×0.017ACSL6
xenobiotic transport1140.4×0.017SLC22A4
response to vitamin D1133.8×0.017SLC22A4
very long-chain fatty acid metabolic process1127.7×0.017ACSL6
acyl-CoA metabolic process1117.0×0.018ACSL6
long-chain fatty acid metabolic process1104.0×0.018ACSL6
response to tumor necrosis factor1104.0×0.018SLC22A5
lysosome localization187.8×0.018RNF167
response to type II interferon187.8×0.018SLC22A5
response to exogenous dsRNA187.8×0.018SLC22A4
regulation of Rho protein signal transduction185.1×0.018DOCK6
regulation of synaptic transmission, glutamatergic185.1×0.018RNF167
liver regeneration185.1×0.018SLC22A4

Therapeutics

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 7

Druggability breadth: 3 of 7 evidence-associated genes (43%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

SymbolMoleculesMax phase
SLC22A500
SLC22A400
ZBTB1800
ACSL600
DOCK600
RNF16700
MIR3936HG00

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

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

SymbolAssaysType breakdown
SLC22A597Functional:79, ADMET:18
SLC22A429Functional:26, ADMET:3
ACSL61Binding:1

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
ACSL66.2.1.3long-chain-fatty-acid-CoA ligase

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

0 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.

Druggability pyramid

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

TierDefinitionGenesSymbols
AApproved (phase 4 drug)0
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug1SLC22A5
DDruggable family + AlphaFold only, no drug2SLC22A4, ACSL6
EDifficult family or no structure, no drug4ZBTB18, DOCK6, RNF167, MIR3936HG

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
SLC22A597
SLC22A429
ZBTB180
ACSL61
DOCK60
RNF1670
MIR3936HG0

Clinical trials & evidence

Clinical trials

Clinical trials: 6.

Phase distribution (across all retrieved trials)

PhaseTrials
Not specified3
PHASE41
PHASE2/PHASE31
EARLY_PHASE11

Top trials by phase / activity

NCTPhaseStatusTitle
NCT01904396PHASE4UNKNOWNIdentification of Carnitine-Responsive Cardiomyopathy
NCT01783041PHASE2/PHASE3COMPLETEDEffect of Early L-Carnitine Supplementation on Neurodevelopmental Outcomes in Very Preterm Infants
NCT07201714EARLY_PHASE1RECRUITINGOral Carnitine in Heart Failure Patients
NCT00187733Not specifiedCOMPLETEDInfluence of OCTN2 Variants on Carnitine Status and Plasma Triglycerides
NCT02635269Not specifiedUNKNOWNFat and Sugar Metabolism During Exercise in Patients With Metabolic Myopathy
NCT05910151Not specifiedUNKNOWNSelective Screening of Children for Hereditary Metabolic Diseases by Tandem Mass Spectrometry in Kazakhstan

Drugs tested across these trials (top 30)

MoleculeMax phaseTrials referencing
LEVOCARNITINE43
CARNITINE32
DEXTROCARNITINE01