Creatine transporter deficiency

disease
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Also known as CCDS1cerebral creatine deficiency syndrome 1cerebral creatine deficiency syndrome 1, X-linked recessivecerebral creatine deficiency syndrome type 1creatine deficiency, X-linkedintellectual disability, X-linked with seizures, short stature and midface hypoplasiaintellectual disability, X-linked, with creatine transport deficiencymental retardation, X-linked with seizures, short stature and midface hypoplasiamental retardation, X-linked, with creatine Transport deficiencymental retardation, X-linked, with seizures, short stature, and midface hypoplasiaSLC6A8 deficiencyX-linked creatine deficiencyX-linked creatine deficiency syndrome

Summary

Creatine transporter deficiency (MONDO:0010305) is a disease caused by SLC6A8 (GenCC Definitive), with 4 cohort genes and 6 clinical trials.

At a glance

  • Prevalence: Unknown (Worldwide) [Orphanet-validated]
  • Causal gene: SLC6A8 (GenCC Definitive)
  • Cohort genes: 4
  • ClinVar variants: 1,069
  • Phenotypes (HPO): 26
  • Clinical trials: 6

Clinical features

Epidemiology

Prevalence records

1 prevalence record(s), Orphanet:

TypeClassValueGeographyValidation
Cases/families150WorldwideValidated

Signs & symptoms

Clinical features (HPO)

26 HPO clinical features (Orphanet curated; top 26 by frequency):

HPO IDTermFrequency
HP:0000750Delayed speech and language developmentVery frequent (80-99%)
HP:0001249Intellectual disabilityVery frequent (80-99%)
HP:0001250SeizureVery frequent (80-99%)
HP:0001263Global developmental delayVery frequent (80-99%)
HP:0012113Abnormality of creatine metabolismVery frequent (80-99%)
HP:0000194Open mouthFrequent (30-79%)
HP:0000272Malar flatteningFrequent (30-79%)
HP:0000729Autistic behaviorFrequent (30-79%)
HP:0000742Self-mutilationFrequent (30-79%)
HP:0001251AtaxiaFrequent (30-79%)
HP:0001252HypotoniaFrequent (30-79%)
HP:0001276HypertoniaFrequent (30-79%)
HP:0001332DystoniaFrequent (30-79%)
HP:0002019ConstipationFrequent (30-79%)
HP:0002072ChoreaFrequent (30-79%)
HP:0000752HyperactivityFrequent (30-79%)
HP:0002251Aganglionic megacolonFrequent (30-79%)
HP:0002305AthetosisFrequent (30-79%)
HP:0002595IleusFrequent (30-79%)
HP:0004322Short statureFrequent (30-79%)
HP:0004326CachexiaFrequent (30-79%)
HP:0000252MicrocephalyOccasional (5-29%)
HP:0000298Mask-like faciesOccasional (5-29%)
HP:0000508PtosisOccasional (5-29%)
HP:0001582Redundant skinOccasional (5-29%)
HP:0001382Joint hypermobilityOccasional (5-29%)

Identifiers

Disease identifiers

FieldValue
Canonical namecreatine transporter deficiency
Mondo IDMONDO:0010305
MeSHC535598
OMIM300352
Orphanet52503
DOIDDOID:0050800
NCITC125665
SNOMED CT698290008
UMLSC1845862
MedGen337451
GARD0001608
NORD1966
Is cancer (heuristic)no

Also known as: CCDS1 · cerebral creatine deficiency syndrome 1 · cerebral creatine deficiency syndrome 1, X-linked recessive · cerebral creatine deficiency syndrome type 1 · creatine deficiency, X-linked · creatine transporter deficiency · intellectual disability, X-linked with seizures, short stature and midface hypoplasia · intellectual disability, X-linked, with creatine transport deficiency · mental retardation, X-linked with seizures, short stature and midface hypoplasia · mental retardation, X-linked, with creatine Transport deficiency · mental retardation, X-linked, with creatine transport deficiency · mental retardation, X-linked, with seizures, short stature, and midface hypoplasia · SLC6A8 deficiency · X-linked creatine deficiency · X-linked creatine deficiency syndrome

Data availability: 1,069 ClinVar variants · 174 ClinGen variant curations · 5 GenCC gene-disease records · 32 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 metabolismcerebral creatine deficiency syndromecreatine transporter deficiency

Related subtypes (2): AGAT deficiency, guanidinoacetate methyltransferase deficiency

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:

336 likely benign, 124 uncertain significance, 53 pathogenic, 37 benign, 25 likely pathogenic, 14 benign/likely benign, 9 conflicting classifications of pathogenicity, 2 pathogenic/likely pathogenic

ClinVarVariant (HGVS)GeneClassificationReview
2422157NC_000023.10:g.(?152014869)(155171615_?)delABCD1Pathogeniccriteria provided, single submitter
1064525NM_005629.4(SLC6A8):c.1394_1399del (p.Gly465_Met467delinsVal)SLC6A8Pathogenicno assertion criteria provided
1069434NM_005629.4(SLC6A8):c.1108C>T (p.Gln370Ter)SLC6A8Pathogeniccriteria provided, multiple submitters, no conflicts
1070967NM_005629.4(SLC6A8):c.1551del (p.Trp518fs)SLC6A8Pathogeniccriteria provided, single submitter
1076955NM_005629.4(SLC6A8):c.1393-12_1395delSLC6A8Pathogeniccriteria provided, single submitter
11696NM_005629.4(SLC6A8):c.1540C>T (p.Arg514Ter)SLC6A8Pathogenicreviewed by expert panel
11697NM_005629.4(SLC6A8):c.1141G>C (p.Gly381Arg)SLC6A8Pathogenicreviewed by expert panel
11698NM_005629.4(SLC6A8):c.1216TTC[2] (p.Phe408del)SLC6A8Pathogenicreviewed by expert panel
11699NM_005629.4(SLC6A8):c.950dup (p.Tyr317Ter)SLC6A8Pathogenicreviewed by expert panel
11701NM_005629.4(SLC6A8):c.263-2A>GSLC6A8Pathogenicreviewed by expert panel
11702NM_005629.4(SLC6A8):c.1011C>G (p.Cys337Trp)SLC6A8Pathogenicno assertion criteria provided
1174596NM_005629.4(SLC6A8):c.1016+2_1016+5delSLC6A8Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1308664NM_005629.4(SLC6A8):c.1330G>T (p.Glu444Ter)SLC6A8Pathogeniccriteria provided, single submitter
1361089NM_005629.4(SLC6A8):c.1169C>T (p.Pro390Leu)SLC6A8Pathogenicreviewed by expert panel
1376685NM_005629.4(SLC6A8):c.1283del (p.Gly428fs)SLC6A8Pathogeniccriteria provided, single submitter
1390569NM_005629.4(SLC6A8):c.453_454insGCTGAGGCGGGAGAATCTCTTGAAGCCGGGAAGCAGAGGTTGCAGTGAACCGACATCGCGCCACTGCACTCCAGCCTGGGTGACAGAGTGAGACTCCATCTCAAAATAAATAAAAATAAAATAAAATAAAACAAGGTCTCATTCTCTTACCCAGGCTGGAGTGCAGTGGTACAATCAGAGCTCACCCCAGCCACAAACTCCTGGACTCAAGTGATCCTCCCACCTCAGCCTCCCTTGAATAGCTAGGACTACAAGTGTATGCCTCCAGGCCTGGCTAATTGTTTTTAATTTTTTGGTAGAGGCAGGGATCTCATTGTATTGCCCAGGCTGGGGTCCCAAACTCCTGATCACAAGTGAACCTCCTGCCTCAGCCTCTGAAAGTGCTGGGATTACAGGCATGAGCCACCGTGCCCAGCTCCCTGACAATTTCTGGCTGCATGGACTTCTGGTTACAAGCAGGGAAACTGAGGCCTGGATACAGCAAACAGGATCTGGCCCAGCTTTAAGTGGGGAACATGCAGTTTGGGGGACCCAGGCTCATGGTG (p.Leu152delinsAlaGluAlaGlyGluSerLeuGluAlaGlyLysGlnArgLeuGlnTer)SLC6A8Pathogeniccriteria provided, single submitter
1395238NM_005629.4(SLC6A8):c.1496-1_1510delSLC6A8Pathogeniccriteria provided, single submitter
1397100NM_005629.4(SLC6A8):c.444_445del (p.Ile149fs)SLC6A8Pathogeniccriteria provided, single submitter
1412467NM_005629.4(SLC6A8):c.1055G>A (p.Ser352Asn)SLC6A8Pathogeniccriteria provided, single submitter
1416517NM_005629.4(SLC6A8):c.1037_1038del (p.Leu346fs)SLC6A8Pathogeniccriteria provided, single submitter
1417554NM_005629.4(SLC6A8):c.1210del (p.Ala404fs)SLC6A8Pathogeniccriteria provided, single submitter
1429550NM_005629.4(SLC6A8):c.844del (p.Leu282fs)SLC6A8Pathogeniccriteria provided, single submitter
1679707NM_005629.4(SLC6A8):c.627del (p.Val210fs)SLC6A8Pathogeniccriteria provided, single submitter
1686215NM_005629.4(SLC6A8):c.980dup (p.Ser329fs)SLC6A8Pathogeniccriteria provided, single submitter
1687062NM_005629.4(SLC6A8):c.1292_1302del (p.Asp431fs)SLC6A8Pathogeniccriteria provided, single submitter
1703957NM_005629.4(SLC6A8):c.1519_1543del (p.Ile507fs)SLC6A8Pathogenicreviewed by expert panel
1705030NM_005629.4(SLC6A8):c.1548C>A (p.Cys516Ter)SLC6A8Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1706458NM_005629.4(SLC6A8):c.1340_1341del (p.Val447fs)SLC6A8Pathogeniccriteria provided, multiple submitters, no conflicts
1802549NM_005629.4(SLC6A8):c.1428C>G (p.Tyr476Ter)SLC6A8Pathogenicreviewed by expert panel
1804054NM_005629.4(SLC6A8):c.149dup (p.Pro51fs)SLC6A8Pathogeniccriteria provided, single submitter

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 5 · Orphanet: 8 · 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
SLC6A8DefinitiveX-linkedcreatine transporter deficiency5

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
SLC6A8Orphanet:52503X-linked creatine transporter deficiency
BCAP31Orphanet:369939Severe motor and intellectual disabilities-sensorineural deafness-dystonia syndrome
BCAP31Orphanet:369942CADDS
ABCD1Orphanet:139396X-linked cerebral adrenoleukodystrophy
ABCD1Orphanet:139399Adrenomyeloneuropathy
ABCD1Orphanet:369942CADDS
ABCD1Orphanet:388Hirschsprung disease
ATP2B3Orphanet:314978X-linked non progressive cerebellar ataxia

Cohort genes → proteins

4 cohort genes, 4 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence4

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
SLC6A8HGNC:11055ENSG00000130821P48029Sodium- and chloride-dependent creatine transporter 1gencc,clinvar
BCAP31HGNC:16695ENSG00000185825P51572B-cell receptor-associated protein 31clinvar
ABCD1HGNC:61ENSG00000101986P33897ATP-binding cassette sub-family D member 1clinvar
ATP2B3HGNC:816ENSG00000067842Q16720Plasma membrane calcium-transporting ATPase 3clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
SLC6A8Sodium- and chloride-dependent creatine transporter 1Creatine:sodium symporter which mediates the uptake of creatine.
BCAP31B-cell receptor-associated protein 31Functions as a chaperone protein.
ABCD1ATP-binding cassette sub-family D member 1ATP-dependent transporter of the ATP-binding cassette (ABC) family involved in the transport of very long chain fatty acid (VLCFA)-CoA from the cytosol to the peroxisome lumen.
ATP2B3Plasma membrane calcium-transporting ATPase 3ATP-driven Ca(2+) ion pump involved in the maintenance of basal intracellular Ca(2+) levels at the presynaptic terminals.

Protein-family classification

Druggable: 1 · Difficult: 1 · Unknown: 2 · Druggable fraction: 0.25

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
Transporter119.4×0.151
Transcription factor12.1×0.605
Other/Unknown20.9×0.769

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
SLC6A8Other/UnknownnoNa/ntran_symport, Na/ntran_symport_creatine, SNS_sf
BCAP31Other/UnknownnoBAP29/BAP31, BAP29/BAP31_N, Bap31/Bap29_C
ABCD1Transporteryes7.6.2.4ABC_transporter-like_ATP-bd, AAA+_ATPase, FA_transporter
ATP2B3Transcription factorno7.2.2.10P_typ_ATPase, ATPase_P-typ_cation-transptr_N, ATPase_P-typ_cation-transptr_C

Expression context

Cohort genes with no expression data: 0.

3 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)4
unknown0

Top tissues across cohort

TissueCohort genes
ileal mucosa2
left adrenal gland2
apex of heart1
inferior olivary complex1
right adrenal gland1
right adrenal gland cortex1
left adrenal gland cortex1
Brodmann (1909) area 231
endothelial cell1
middle temporal gyrus1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
SLC6A8291ubiquitousmarkerinferior olivary complex, apex of heart, ileal mucosa
BCAP31292ubiquitousmarkerleft adrenal gland, right adrenal gland, right adrenal gland cortex
ABCD1201ubiquitousmarkerileal mucosa, left adrenal gland cortex, left adrenal gland
ATP2B3145tissue_specificyesendothelial cell, Brodmann (1909) area 23, middle temporal gyrus

Protein interactions among cohort

Intra-cohort edges: 1.

Hub genes (top 10 by interactor count)

SymbolInteractor count
ATP2B33,203
BCAP313,085
SLC6A81,508
ABCD11,181

Intra-cohort edges

ABSources
ABCD1BCAP31string_interaction

Structural data

PDB: 3 · AlphaFold-only: 1 · No structure: 0

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
ABCD1P3389714
SLC6A8P480296
BCAP31P515723

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
ATP2B3Q1672074.57

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 45. Enrichment computed across 4 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
Defective ABCD1 causes ALD11427.5×0.027ABCD1
alpha-linolenic (omega3) and linoleic (omega6) acid metabolism1475.8×0.027ABCD1
Linoleic acid (LA) metabolism1285.5×0.027ABCD1
Creatine metabolism1259.6×0.027SLC6A8
Reduction of cytosolic Ca++ levels1237.9×0.027ATP2B3
Beta-oxidation of very long chain fatty acids1219.6×0.027ABCD1
alpha-linolenic acid (ALA) metabolism1178.4×0.027ABCD1
Platelet calcium homeostasis1178.4×0.027ATP2B3
Peroxisomal lipid metabolism1167.9×0.027ABCD1
ABC transporters in lipid homeostasis1150.3×0.027ABCD1
Class I peroxisomal membrane protein import1129.8×0.027ABCD1
Apoptotic cleavage of cellular proteins1119.0×0.027BCAP31
Apoptotic execution phase1119.0×0.027BCAP31
ABC transporter disorders1109.8×0.027ABCD1
Transport of small molecules212.6×0.027ABCD1, ATP2B3
Antigen Presentation: Folding, assembly and peptide loading of class I MHC198.5×0.028BCAP31
Platelet homeostasis169.6×0.038ATP2B3
Ion transport by P-type ATPases151.9×0.045ATP2B3
Ion homeostasis151.0×0.045ATP2B3
Respiratory Syncytial Virus Infection Pathway149.2×0.045BCAP31
Protein localization147.6×0.045ABCD1
Apoptosis142.0×0.048BCAP31
RSV-host interactions139.1×0.050BCAP31
Programmed Cell Death136.6×0.051BCAP31
Disorders of transmembrane transporters134.8×0.051ABCD1
Fatty acid metabolism132.8×0.052ABCD1
ABC-family protein mediated transport130.4×0.052ABCD1
Disease26.5×0.052BCAP31, ABCD1
Cardiac conduction127.2×0.056ATP2B3
Metabolism25.8×0.059SLC6A8, ABCD1

GO biological processes 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.

GO termCohort genesFoldFDRSample cohort genes
peroxisomal membrane transport12106.5×0.005ABCD1
very long-chain fatty-acyl-CoA catabolic process12106.5×0.005ABCD1
positive regulation of retrograde protein transport, ER to cytosol11404.3×0.005BCAP31
positive regulation of unsaturated fatty acid biosynthetic process11404.3×0.005ABCD1
creatine metabolic process11053.2×0.005SLC6A8
creatine transmembrane transport11053.2×0.005SLC6A8
sterol homeostasis11053.2×0.005ABCD1
long-chain fatty acid import into peroxisome1842.6×0.005ABCD1
regulation of fatty acid beta-oxidation1702.2×0.005ABCD1
long-chain fatty acid catabolic process1702.2×0.005ABCD1
myelin maintenance1702.2×0.005ABCD1
regulation of mitochondrial depolarization1702.2×0.005ABCD1
calcium ion export across plasma membrane1702.2×0.005ATP2B3
fatty acid elongation1601.9×0.005ABCD1
very long-chain fatty acid catabolic process1601.9×0.005ABCD1
protein localization to endoplasmic reticulum exit site1526.6×0.006BCAP31
positive regulation of fatty acid beta-oxidation1383.0×0.007ABCD1
fatty acid derivative biosynthetic process1383.0×0.007ABCD1
regulation of cellular response to oxidative stress1324.1×0.008ABCD1
regulation of oxidative phosphorylation1300.9×0.008ABCD1
neuron projection maintenance1280.9×0.008ABCD1
negative regulation of reactive oxygen species biosynthetic process1247.8×0.008ABCD1
fatty acid homeostasis1234.1×0.008ABCD1
alpha-linolenic acid metabolic process1221.7×0.008ABCD1
positive regulation of ERAD pathway1221.7×0.008BCAP31
regulation of cardiac conduction1210.7×0.009ATP2B3
peroxisome organization1200.6×0.009ABCD1
very long-chain fatty acid metabolic process1191.5×0.009ABCD1
linoleic acid metabolic process1175.5×0.009ABCD1
unsaturated fatty acid biosynthetic process1162.0×0.010ABCD1

Therapeutics

Drug target analysis

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

Druggability breadth: 2 of 4 evidence-associated genes (50%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

SymbolMoleculesMax phase
SLC6A813
BCAP3100
ABCD100
ATP2B300

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
CREATINE3SLC6A8

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 2.

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

SymbolAssaysType breakdown
BCAP318Binding:8
SLC6A81Functional:1

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
ABCD17.6.2.4ABC-type fatty-acyl-CoA transporter
ATP2B37.2.2.10P-type Ca2+ transporter

Pharmacogenomics

Cohort genes with a PharmGKB record: 4; 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)
CREATINE3SLC6A8

Druggability pyramid

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

TierDefinitionGenesSymbols
AApproved (phase 4 drug)0
BPhased (≥1) drug, not yet approved1SLC6A8
CDruggable family + PDB, no drug1ABCD1
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug2BCAP31, ATP2B3

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
BCAP318
ABCD10
ATP2B30

Clinical trials & evidence

Clinical trials

Clinical trials: 6.

Phase distribution (across all retrieved trials)

PhaseTrials
Not specified6

Top trials by phase / activity

NCTPhaseStatusTitle
NCT03655223Not specifiedENROLLING_BY_INVITATIONEarly Check: Expanded Screening in Newborns
NCT06139172Not specifiedRECRUITINGWeb Intervention for Parents of Youth With Genetic Syndromes (WINGS)
NCT06868979Not specifiedRECRUITINGOptical Imaging in X-linked Disorders.
NCT02931682Not specifiedTERMINATEDObservational Study of Males With Creatine Transporter Deficiency
NCT05642221Not specifiedCOMPLETEDFunctional Near-Infrared Spectroscopy (fNIRS) Combined With Diffuse Correlation Spectroscopy (DCS) in Neurocognitive Disease as Compared to Healthy Neurotypical Controls
NCT06292884Not specifiedUNKNOWNOptical Imaging as a Tool for Monitoring Brain Function in Creatine Deficiency Syndromes