Agenesis of the corpus callosum with peripheral neuropathy

disease
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Also known as ACCPNagenesis of corpus callosum with neuronopathyagenesis of corpus callosum with peripheral neuropathyagenesis of corpus callosum with polyneuropathyAndermann syndromeCharlevoix diseasecorpus callosum agenesis neuronopathycorpus callosum agenesis-neuronopathy syndromehereditary motor and sensory neuropathy with agenesis of the corpus callosumHMSN/ACCperipheral neuropathy associated with agenesis of the corpus callosum

Summary

Agenesis of the corpus callosum with peripheral neuropathy (MONDO:0000902) is a disease caused by SLC12A6 (GenCC Definitive), with 4 cohort genes.

At a glance

  • Prevalence: 1-5 / 10 000 (Specific population) [Orphanet-validated]
  • Causal gene: SLC12A6 (GenCC Definitive)
  • Cohort genes: 4
  • ClinVar variants: 475
  • Phenotypes (HPO): 14

Clinical features

Epidemiology

Prevalence records

2 prevalence record(s), Orphanet:

TypeClassValueGeographyValidation
Point prevalence1-5 / 10 00047Specific populationValidated
Point prevalence<1 / 1 000 000WorldwideNot yet validated

Signs & symptoms

Clinical features (HPO)

14 HPO clinical features (Orphanet curated; top 14 by frequency):

HPO IDTermFrequency
HP:0000252MicrocephalyVery frequent (80-99%)
HP:0001249Intellectual disabilityVery frequent (80-99%)
HP:0001250SeizureVery frequent (80-99%)
HP:0001263Global developmental delayVery frequent (80-99%)
HP:0001274Agenesis of corpus callosumVery frequent (80-99%)
HP:0002353EEG abnormalityVery frequent (80-99%)
HP:0004374Hemiplegia/hemiparesisVery frequent (80-99%)
HP:0002410Aqueductal stenosisFrequent (30-79%)
HP:0000262TurricephalyOccasional (5-29%)
HP:0000486StrabismusOccasional (5-29%)
HP:0000545MyopiaOccasional (5-29%)
HP:0000639NystagmusOccasional (5-29%)
HP:0001363CraniosynostosisOccasional (5-29%)
HP:0007703Abnormality of retinal pigmentationOccasional (5-29%)

Identifiers

Disease identifiers

FieldValue
Canonical nameagenesis of the corpus callosum with peripheral neuropathy
Mondo IDMONDO:0000902
MeSHC536446
OMIM218000
Orphanet1496
DOIDDOID:0060600, DOID:0090003
ICD-111443432032
SNOMED CT702439002
UMLSC0795950
MedGen162893
GARD0001537
Is cancer (heuristic)no

Also known as: ACCPN · agenesis of corpus callosum with neuronopathy · agenesis of corpus callosum with peripheral neuropathy · agenesis of corpus callosum with polyneuropathy · agenesis of the corpus callosum with peripheral neuropathy · Andermann syndrome · Charlevoix disease · corpus callosum agenesis neuronopathy · corpus callosum agenesis-neuronopathy syndrome · hereditary motor and sensory neuropathy with agenesis of the corpus callosum · HMSN/ACC · peripheral neuropathy associated with agenesis of the corpus callosum

Data availability: 475 ClinVar variants · 5 GenCC gene-disease records.

Disease family

Classification path: disease › human disease › disease by body system or component › nervous system disordercentral nervous system disorderneurodegenerative diseaseinherited neurodegenerative disorderagenesis of the corpus callosum with peripheral neuropathy

Related subtypes (81): Huntington disease and related disorders, striatonigral degeneration, angioid streaks of choroid, amyotrophic lateral sclerosis-parkinsonism-dementia complex, inherited Creutzfeldt-Jakob disease, mitochondrial DNA depletion syndrome 4a, cerebellar ataxia-hypogonadism syndrome, myoclonic cerebellar dyssynergia, cerebral sclerosis similar to Pelizaeus-Merzbacher disease, Chediak-Higashi syndrome, encephalopathy due to beta-mercaptolactate-cysteine disulfiduria, PEHO syndrome, deafness dystonia syndrome, Kennedy disease, fatal familial insomnia, Huntington disease-like 1, neuronal intranuclear inclusion disease, ataxia-telangiectasia-like disorder, radiation sensitivity/chromosome instability syndrome, autosomal dominant, Huntington disease-like 2, microphthalmia-brain atrophy syndrome, neurodegenerative syndrome due to cerebral folate transport deficiency, hereditary sensory neuropathy-deafness-dementia syndrome, infantile cerebellar-retinal degeneration, Alzheimer disease 17, hypotonia, infantile, with psychomotor retardation and characteristic facies, Alzheimer disease 18, diffuse cerebral and cerebellar atrophy - intractable seizures - progressive microcephaly syndrome, severe neurodegenerative syndrome with lipodystrophy, developmental and epileptic encephalopathy, 35, combined oxidative phosphorylation deficiency 29, neurodegeneration with ataxia, dystonia, and gaze palsy, childhood-onset, encephalopathy, progressive, early-onset, with brain edema and/or leukoencephalopathy, dystonia, childhood-onset, with optic atrophy and basal ganglia abnormalities, neuronal ceroid lipofuscinosis, frontotemporal dementia with motor neuron disease, frontotemporal dementia, GM2 gangliosidosis, attenuated Chédiak-Higashi syndrome, autosomal recessive cerebral atrophy, neurodegeneration with brain iron accumulation, fatal post-viral neurodegenerative disorder, ferro-cerebro-cutaneous syndrome, PRKAR1B-related neurodegenerative dementia with intermediate filaments, ITM2B amyloidosis, corticobasal syndrome, infantile-onset axonal motor and sensory neuropathy-optic atrophy-neurodegenerative syndrome, recurrent metabolic encephalomyopathic crises-rhabdomyolysis-cardiac arrhythmia-intellectual disability syndrome, posterior cortical atrophy, progressive supranuclear palsy, leukodystrophy, hereditary spastic paraplegia, facial onset sensory and motor neuronopathy, X-linked neurodegenerative syndrome, Bertini type, X-linked neurodegenerative syndrome, Hamel type, boylan dew greco syndrome, hereditary motor neuron disease, neurodegeneration, childhood-onset, with ataxia, tremor, optic atrophy, and cognitive decline, frontotemporal dementia and/or amyotrophic lateral sclerosis, neurodegeneration, childhood-onset, with hypotonia, respiratory insufficiency, and brain imaging abnormalities, neurodegeneration with ataxia and late-onset optic atrophy, neurodegeneration, childhood-onset, with cerebellar atrophy, neurodegeneration, early-onset, with choreoathetoid movements and microcytic anemia, neurodegeneration, infantile-onset, biotin-responsive, hereditary optic atrophy, early-onset progressive diffuse brain atrophy-microcephaly-muscle weakness-optic atrophy syndrome, psychomotor regression-oculomotor apraxia-movement disorder-nephropathy syndrome, familial Alzheimer disease, neurodegeneration, childhood-onset, stress-induced, with variable ataxia and seizures, hereditary cerebellar ataxia, DCTN1-related neurodegeneration, early-childhood-onset neurodegeneration with retinitis pigmentosa, sensorineural hearing loss, and demyelinating peripheral neuropathy, TUBB4A-related neurologic disorder, neurodegeneration, childhood-onset, with progressive microcephaly, neurodegeneration, childhood-onset, with multisystem involvement due to mitochondrial dysfunction, neurodegeneration and seizures due to copper transport defect, neurodegeneration with developmental delay, early respiratory failure, myoclonic seizures, and brain abnormalities, neurodegeneration, childhood-onset, with cerebellar ataxia and cognitive decline, neurodegenerative disorder, X-linked, female-restricted, with parkinsonism and cognitive impairment, neurodegenerative disorder with cerebellar and caudate atrophy, APP-related brain and vascular amyloidosis

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

475 retrieved; paginated sample, class counts are floors:

184 uncertain significance, 118 likely pathogenic, 49 likely benign, 43 benign, 27 conflicting classifications of pathogenicity, 25 pathogenic/likely pathogenic, 17 pathogenic, 12 benign/likely benign

ClinVarVariant (HGVS)GeneClassificationReview
1068924NM_001365088.1(SLC12A6):c.2509_2510insTC (p.Glu837fs)LOC126862097Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
3366315NM_001365088.1(SLC12A6):c.690+6T>ALOC129390683Pathogeniccriteria provided, single submitter
370396NM_001365088.1(SLC12A6):c.655C>T (p.Gln219Ter)LOC129390683Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1029940NM_001365088.1(SLC12A6):c.2230C>T (p.Arg744Ter)SLC12A6Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1029941NM_001365088.1(SLC12A6):c.1151C>G (p.Ser384Ter)SLC12A6Pathogeniccriteria provided, single submitter
1072743NM_001365088.1(SLC12A6):c.776del (p.Ala259fs)SLC12A6Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1075166NM_001365088.1(SLC12A6):c.892C>T (p.Arg298Ter)SLC12A6Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
136175NM_001365088.1(SLC12A6):c.1584_1585delinsG (p.Phe529fs)SLC12A6Pathogenicno assertion criteria provided
136176NM_001365088.1(SLC12A6):c.2032dup (p.Tyr678fs)SLC12A6Pathogenicno assertion criteria provided
136177NM_001365088.1(SLC12A6):c.1478_1485del (p.Phe493fs)SLC12A6Pathogenicno assertion criteria provided
1388798NM_001365088.1(SLC12A6):c.2893dup (p.Tyr965fs)SLC12A6Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1451911NM_001365088.1(SLC12A6):c.2962_2963dup (p.Glu989fs)SLC12A6Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1452914NM_001365088.1(SLC12A6):c.2710G>T (p.Glu904Ter)SLC12A6Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
159897NM_001365088.1(SLC12A6):c.379G>T (p.Glu127Ter)SLC12A6Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1705184NM_001365088.1(SLC12A6):c.1950dup (p.Leu651fs)SLC12A6Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
188972NM_001365088.1(SLC12A6):c.571_572dup (p.Tyr192fs)SLC12A6Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1987661NM_001365088.1(SLC12A6):c.2002C>T (p.Arg668Ter)SLC12A6Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
2678741NM_001365088.1(SLC12A6):c.3321del (p.Asn1107fs)SLC12A6Pathogeniccriteria provided, single submitter
2678744NM_001365088.1(SLC12A6):c.2265G>A (p.Trp755Ter)SLC12A6Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
2678746NM_001365088.1(SLC12A6):c.2180dup (p.Gly727_Asp728insTer)SLC12A6Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
2678754NM_001365088.1(SLC12A6):c.2272C>T (p.Gln758Ter)SLC12A6Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
2678765NM_001365088.1(SLC12A6):c.2736dup (p.Val913fs)SLC12A6Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
2759948NM_001365088.1(SLC12A6):c.1786C>T (p.Gln596Ter)SLC12A6Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
2876293NM_001365088.1(SLC12A6):c.3061C>T (p.Arg1021Ter)SLC12A6Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
30440NM_001365088.1(SLC12A6):c.3400C>T (p.Arg1134Ter)SLC12A6Pathogeniccriteria provided, multiple submitters, no conflicts
3240465NM_001365088.1(SLC12A6):c.3361+1G>CSLC12A6Pathogeniccriteria provided, single submitter
370137NM_001365088.1(SLC12A6):c.2809C>T (p.Arg937Ter)SLC12A6Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
370139NM_001365088.1(SLC12A6):c.1118+1G>ASLC12A6Pathogeniccriteria provided, multiple submitters, no conflicts
370269NM_001365088.1(SLC12A6):c.298G>T (p.Glu100Ter)SLC12A6Pathogeniccriteria provided, single submitter
370595NM_001365088.1(SLC12A6):c.963C>A (p.Tyr321Ter)SLC12A6Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 7 · Orphanet: 5 · 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
SLC12A6DefinitiveAutosomal recessiveagenesis of the corpus callosum with peripheral neuropathy7

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
SLC12A6Orphanet:1496Corpus callosum agenesis-neuronopathy syndrome
CLN6Orphanet:700467Late infantile CLN6 disease
CLN6Orphanet:700472Juvenile CLN6 disease
CLN6Orphanet:700477Adult CLN6 disease
ATP2B2Orphanet:90636Rare autosomal recessive non-syndromic sensorineural deafness type DFNB

Cohort genes → proteins

4 cohort genes, 4 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence4

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
SLC12A6HGNC:10914ENSG00000140199Q9UHW9Solute carrier family 12 member 6gencc,clinvar
CLN6HGNC:2077ENSG00000128973Q9NWW5Ceroid-lipofuscinosis neuronal protein 6clinvar
EMC4HGNC:28032ENSG00000128463Q5J8M3ER membrane protein complex subunit 4clinvar
ATP2B2HGNC:815ENSG00000157087Q01814Plasma membrane calcium-transporting ATPase 2clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
SLC12A6Solute carrier family 12 member 6Mediates electroneutral potassium-chloride cotransport when activated by cell swelling.
EMC4ER membrane protein complex subunit 4Part of the endoplasmic reticulum membrane protein complex (EMC) that enables the energy-independent insertion into endoplasmic reticulum membranes of newly synthesized membrane proteins.
ATP2B2Plasma membrane calcium-transporting ATPase 2ATP-driven Ca(2+) ion pump involved in the maintenance of basal intracellular Ca(2+) levels in specialized cells of cerebellar circuit and vestibular and cochlear systems.

Protein-family classification

Druggable: 0 · Difficult: 1 · Unknown: 3 · Druggable fraction: 0.0

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
Transcription factor12.1×0.404
Other/Unknown31.3×0.404

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
SLC12A6Other/UnknownnoKCL_cotranspt, AA-permease/SLC12A_dom, SLC12A_fam
CLN6Other/UnknownnoCLN6
EMC4Other/UnknownnoTMEM85/Emc4
ATP2B2Transcription 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.

4 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
blood1
esophagus squamous epithelium1
secondary oocyte1
bone marrow1
leukocyte1
monocyte1
calcaneal tendon1
left ventricle myocardium1
upper arm skin1
Brodmann (1909) area 461
endothelial cell1
lateral nuclear group of thalamus1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
SLC12A6274ubiquitousmarkeresophagus squamous epithelium, blood, secondary oocyte
CLN6139ubiquitousmarkermonocyte, leukocyte, bone marrow
EMC4260ubiquitousmarkerleft ventricle myocardium, calcaneal tendon, upper arm skin
ATP2B2203tissue_specificmarkerlateral nuclear group of thalamus, endothelial cell, Brodmann (1909) area 46

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

SymbolInteractor count
ATP2B23,932
EMC42,120
SLC12A61,463
CLN61,107

Structural data

PDB: 2 · AlphaFold-only: 2 · No structure: 0

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
EMC4Q5J8M39
SLC12A6Q9UHW98

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
CLN6Q9NWW585.86
ATP2B2Q0181473.83

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 20. Enrichment computed across 4 evidence-associated genes (3 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 3 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Defective SLC12A6 causes agenesis of the corpus callosum, with peripheral neuropathy (ACCPN)13806.7×0.005SLC12A6
Cation-coupled Chloride cotransporters1543.8×0.018SLC12A6
Reduction of cytosolic Ca++ levels1317.2×0.018ATP2B2
Platelet calcium homeostasis1237.9×0.018ATP2B2
Transport of small molecules216.8×0.018SLC12A6, ATP2B2
Platelet homeostasis192.8×0.027ATP2B2
Dengue Virus Attachment and Entry186.5×0.027EMC4
Ion transport by P-type ATPases169.2×0.027ATP2B2
Ion homeostasis168.0×0.027ATP2B2
SLC transporter disorders168.0×0.027SLC12A6
Sensory processing of sound by outer hair cells of the cochlea168.0×0.027ATP2B2
Sensory processing of sound by inner hair cells of the cochlea154.4×0.030ATP2B2
Disorders of transmembrane transporters146.4×0.033SLC12A6
R-HSA-425393143.3×0.033SLC12A6
Cardiac conduction136.2×0.036ATP2B2
Ion channel transport132.0×0.039ATP2B2
Muscle contraction125.7×0.045ATP2B2
SLC-mediated transmembrane transport119.7×0.055SLC12A6
Hemostasis112.0×0.085ATP2B2
Disease14.4×0.212SLC12A6

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
cellular hypotonic salinity response11404.3×0.012SLC12A6
ganglioside metabolic process11053.2×0.012CLN6
glycosaminoglycan metabolic process1601.9×0.012CLN6
locomotion involved in locomotory behavior1601.9×0.012CLN6
protein insertion into ER membrane by stop-transfer membrane-anchor sequence1383.0×0.012EMC4
chloride ion homeostasis1383.0×0.012SLC12A6
cellular hypotonic response1351.1×0.012SLC12A6
tail-anchored membrane protein insertion into ER membrane1234.1×0.014EMC4
regulation of cardiac conduction1210.7×0.014ATP2B2
positive regulation of proteolysis1200.6×0.014CLN6
potassium ion homeostasis1191.5×0.014SLC12A6
lysosomal lumen acidification1168.5×0.015CLN6
cell volume homeostasis1150.5×0.015SLC12A6
regulation of cytosolic calcium ion concentration195.8×0.022ATP2B2
potassium ion import across plasma membrane191.6×0.022SLC12A6
lysosome organization176.6×0.024CLN6
cellular response to glucose stimulus166.9×0.026SLC12A6
protein catabolic process159.3×0.026CLN6
chloride transmembrane transport159.3×0.026SLC12A6
monoatomic ion transmembrane transport152.0×0.029ATP2B2
cholesterol metabolic process149.0×0.029CLN6
calcium ion transport145.3×0.030ATP2B2
monoatomic ion transport139.0×0.033SLC12A6
potassium ion transmembrane transport134.0×0.036SLC12A6
sensory perception of sound125.2×0.045ATP2B2
neuron differentiation125.1×0.045ATP2B2
visual perception119.9×0.054CLN6
chemical synaptic transmission119.3×0.054SLC12A6
angiogenesis115.6×0.065SLC12A6
apoptotic process17.2×0.132EMC4

Therapeutics

Drug target analysis

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

Druggability breadth: 1 of 4 evidence-associated genes (25%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

SymbolMoleculesMax phase
SLC12A600
CLN600
EMC400
ATP2B200

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

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

SymbolAssaysType breakdown
CLN61Binding:1

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
ATP2B27.2.2.10P-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

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 drug0
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug4SLC12A6, CLN6, EMC4, ATP2B2

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
SLC12A60
CLN61
EMC40
ATP2B20

Clinical trials & evidence

Clinical trials

Clinical trials: 0.