Description
Structural basal ganglia disorders inclusion criteria (37789)
•	Patient with structural, preferably symmetrical radiological abnormalities on MR imaging affecting the striatum, globus pallidus and/or substantia nigra, AND
•	Neurological symptoms e.g. movement disorder

Structural basal ganglia disorders exclusion criteria (37789)
•	Evidence of an acquired disorder (e.g. basal ganglia stroke or autoimmune aetiology)
•	No neurological symptoms
•	Known genetic cause

Prior genetic testing guidance (37789)
- Results should have been reviewed for all genetic tests undertaken, including disease-relevant genes in exome sequencing data. The patient is not eligible if they have a molecular diagnosis for their condition. 
- Genetic testing should continue according to routine local practice for this phenotype regardless of recruitment to the project; results of these tests must be submitted via the ‘Genetic investigations’ section of the data capture tool to allow comparison of WGS with current standard testing.  

PLEASE NOTE: The sensitivity of WGS compared to current diagnostic genetic testing has not yet been established. It is therefore important that tests which are clinically indicated under local standard practice continue to be carried out.

Structural basal ganglia disorders prior genetic testing genes (37789)
Testing of the following genes should be carried out PRIOR TO RECRUITMENT where this is in line with current local practice:

- As dictated by phenotype

Closing statement (37789)
These requirements will be kept under continual review during the main programme and may be subject to change.

7 reviewers

  • Ellen McDonagh (Genomics England Curator)

    Group: other
    Workplace: other

  • Carl Fratter (Oxford University Hospitals NHS Trust)

    Group: GeCIP domain
    Workplace: NHS diagnostic lab

  • Manju Kurian (UCL-Institute of Child Health)

    Group: GeCIP domain
    Workplace: NHS clinical service

  • Richard Scott (Genomics England Curator)

    Group: Other
    Workplace: Genomics England

  • Shamima Rahman (UCL Institute of Child Health)

    Group: GeCIP domain
    Workplace: NHS clinical service

  • Sarah Leigh (Genomics England Curator)

    Group: Other
    Workplace: Other

  • Louise Daugherty (Genomics England Curator)

    Group: Other
    Workplace: Other

75 genes

75 reviewed, 63 green

List Gene Reviews Mode of inheritance Details
75 genes
Green Green List (high evidence)
ADAR
2 reviews
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Phenotypes
  • Aicardi-Goutieres syndrome 6 615010
Green Green List (high evidence)
AP1S2
2 reviews
1 green
X-LINKED: hemizygous mutation in males, biallelic mutations in females
Sources
  • Expert Review Green
  • Emory Genetics Laboratory
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Mental retardation, X-linked syndromic 5 304340
Green Green List (high evidence)
ATP13A2
2 reviews
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Phenotypes
  • Kufor-Rakeb syndrome 606693
Green Green List (high evidence)
ATP7B
2 reviews
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Phenotypes
  • Wilson disease 277900
Green Green List (high evidence)
BCS1L
3 reviews
3 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Green Green List (high evidence)
C19orf12
3 reviews
2 green
BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Green Green List (high evidence)
COASY
2 reviews
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Phenotypes
  • Neurodegeneration with brain iron accumulation 6 615643
Green Green List (high evidence)
COX10
4 reviews
2 green 1 red
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Green Green List (high evidence)
COX15
4 reviews
3 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Green Green List (high evidence)
CP
2 reviews
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Phenotypes
  • Cerebellar ataxia 604290
  • Hemosiderosis, systemic, due to aceruloplasminemia 604290
  • [Hypoceruloplasminemia, hereditary] 604290
Green Green List (high evidence)
DLAT
5 reviews
3 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Phenotypes
  • Pyruvate dehydrogenase E2 deficiency 245348
Green Green List (high evidence)
ETHE1
4 reviews
2 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Phenotypes
  • Ethylmalonic encephalopathy 602473
Green Green List (high evidence)
FA2H
2 reviews
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Phenotypes
  • Spastic paraplegia 35, autosomal recessive 612319
Green Green List (high evidence)
FOXP2
2 reviews
1 green
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert Review Green
  • Emory Genetics Laboratory
  • Radboud University Medical Center, Nijmegen
  • Illumina TruGenome Clinical Sequencing Services
Phenotypes
  • Speech-language disorder-1 602081
Green Green List (high evidence)
FTL
1 review
1 green
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Illumina TruGenome Clinical Sequencing Services
  • UKGTN
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Neurodegeneration with brain iron accumulation 3 606159
Green Green List (high evidence)
GCDH
2 reviews
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Green Green List (high evidence)
HIBCH
5 reviews
3 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • Other
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • 3-hydroxyisobutryl-CoA hydrolase deficiency 250620
Green Green List (high evidence)
IFIH1
2 reviews
1 green
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert Review Green
  • UKGTN
Phenotypes
  • Aicardi-Goutieres syndrome 7 615846
Green Green List (high evidence)
ISG15
2 reviews
1 red
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • Other
Phenotypes
  • Immunodeficiency 38 616126
Green Green List (high evidence)
IVD
2 reviews
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Phenotypes
  • Isovaleric acidemia 243500
Green Green List (high evidence)
KMT2B
2 reviews
1 green
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Expert Review Green
Phenotypes
  • Dystonia 28, childhood-onset 617284
Tags
  • treatable
Green Green List (high evidence)
MECR
2 reviews
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Phenotypes
  • Dystonia, childhood-onset, with optic atrophy and basal ganglia abnormalities 617282
Green Green List (high evidence)
MT-ATP6
4 reviews
2 green 1 red
MITOCHONDRIAL
Sources
  • Expert Review Green
Green Green List (high evidence)
MT-ND1
5 reviews
3 green
MITOCHONDRIAL
Sources
  • Expert Review Green
Green Green List (high evidence)
MT-ND6
5 reviews
3 green
MITOCHONDRIAL
Sources
  • Expert Review Green
Green Green List (high evidence)
MUT
2 reviews
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Phenotypes
  • Methylmalonic aciduria, mut(0) type 251000
Green Green List (high evidence)
NDUFA1
4 reviews
1 green 1 red
BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal
Sources
  • Expert Review Green
Phenotypes
  • Mitochondrial complex I deficiency 252010
Green Green List (high evidence)
NDUFA10
3 reviews
2 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Phenotypes
  • Leigh syndrome 256000
Green Green List (high evidence)
NDUFAF2
4 reviews
1 green 1 red
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Green Green List (high evidence)
NDUFAF6
3 reviews
2 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Phenotypes
  • Leigh syndrome due to mitochondrial complex I deficiency 256000
Green Green List (high evidence)
NDUFS4
3 reviews
2 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Phenotypes
  • Leigh syndrome 256000
  • Mitochondrial complex I deficiency 252010
Green Green List (high evidence)
NDUFS7
3 reviews
1 green 1 red
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Green Green List (high evidence)
NDUFS8
3 reviews
2 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Green Green List (high evidence)
NDUFV1
3 reviews
1 green 1 red
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Green Green List (high evidence)
OCLN
2 reviews
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • UKGTN
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Band-like calcification with simplified gyration and polymicrogyria 251290
Green Green List (high evidence)
PANK2
3 reviews
3 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • Expert Review
Green Green List (high evidence)
PCCA
2 reviews
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Phenotypes
  • Propionicacidemia 606054
Green Green List (high evidence)
PCCB
2 reviews
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Phenotypes
  • Propionicacidemia 606054
Green Green List (high evidence)
PDE10A
3 reviews
2 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • Other
Phenotypes
  • Dyskinesia, limb and orofacial, infantile-onset 616921
  • Striatal degeneration, autosomal dominant 616922
Green Green List (high evidence)
PDGFB
2 reviews
1 green
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert Review Green
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Basal ganglia calcification, idiopathic, 5 615483
Green Green List (high evidence)
PDGFRB
2 reviews
1 green
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Emory Genetics Laboratory
  • Expert Review Green
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Basal ganglia calcification, idiopathic, 4 615007
Green Green List (high evidence)
PDHA1
4 reviews
3 green
X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)
Sources
  • Expert Review Green
  • Radboud University Medical Center, Nijmegen
  • Emory Genetics Laboratory
Phenotypes
  • Pyruvate dehydrogenase E1-alpha deficiency 312170
Green Green List (high evidence)
PDP1
5 reviews
3 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Green Green List (high evidence)
PLA2G6
2 reviews
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Phenotypes
  • Infantile neuroaxonal dystrophy 1 256600
  • Neurodegeneration with brain iron accumulation 2B 610217
  • Parkinson disease 14, autosomal recessive 612953
Green Green List (high evidence)
PRNP
1 review
1 green
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Radboud University Medical Center, Nijmegen
  • UKGTN
  • Illumina TruGenome Clinical Sequencing Services
Phenotypes
  • Cerebral amyloid angiopathy, PRNP-related 137440
  • Gerstmann-Straussler disease 137440
  • Huntington disease-like 1 603218
  • Creutzfeldt-Jakob disease 123400
Green Green List (high evidence)
RAB39B
2 reviews
1 red
X-LINKED: hemizygous mutation in males, biallelic mutations in females
Sources
  • Expert Review Green
  • Emory Genetics Laboratory
Phenotypes
  • Waisman syndrome 311510
Green Green List (high evidence)
SDHA
3 reviews
2 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Green Green List (high evidence)
SERAC1
4 reviews
2 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Phenotypes
  • 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome, 614739
  • MEGDEL syndrome
  • 3-MEthylGlutaconic aciduria, Dystonia-Deafness, Hepatopathy, Encephalopathy, Leigh-like syndrome
  • MEGDHEL syndrome
  • Lesions in the basal ganglia
Green Green List (high evidence)
SLC19A3
4 reviews
3 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Emory Genetics Laboratory
  • UKGTN
  • Radboud University Medical Center, Nijmegen
  • Illumina TruGenome Clinical Sequencing Services
Phenotypes
  • Thiamine metabolism dysfunction syndrome 2 (biotin- or thiamine-responsive encephalopathy type 2) 607483
Green Green List (high evidence)
SLC20A2
1 review
1 green
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Radboud University Medical Center, Nijmegen
  • Illumina TruGenome Clinical Sequencing Services
  • Emory Genetics Laboratory
Phenotypes
  • Basal ganglia calcification, idiopathic, 1 213600
Green Green List (high evidence)
SLC25A19
5 reviews
3 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Phenotypes
  • Microcephaly, Amish type 607196
  • Thiamine metabolism dysfunction syndrome 4 (progressive polyneuropathy type) 613710
Green Green List (high evidence)
SLC30A10
2 reviews
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Tags
  • treatable
Green Green List (high evidence)
SLC39A14
2 reviews
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Phenotypes
  • Hypermanganesemia with dystonia 2 617013
Tags
  • treatable
Green Green List (high evidence)
SUCLA2
3 reviews
3 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Green Green List (high evidence)
SUCLG1
3 reviews
3 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Green Green List (high evidence)
SURF1
4 reviews
3 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Green Green List (high evidence)
TOR1A
1 review
1 green
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Illumina TruGenome Clinical Sequencing Services
  • UKGTN
  • Radboud University Medical Center, Nijmegen
  • Emory Genetics Laboratory
Phenotypes
  • Dystonia-1, torsion 128100
Green Green List (high evidence)
TUBA1A
1 review
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Radboud University Medical Center, Nijmegen
  • Illumina TruGenome Clinical Sequencing Services
  • Emory Genetics Laboratory
  • UKGTN
Phenotypes
  • Lissencephaly 3 611603
Green Green List (high evidence)
TUBB4A
2 reviews
1 green
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert Review Green
  • Radboud University Medical Center, Nijmegen
  • Illumina TruGenome Clinical Sequencing Services
Phenotypes
  • Leukodystrophy, hypomyelinating, 6 612438
Green Green List (high evidence)
VAC14
2 reviews
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Phenotypes
  • Striatonigral degeneration, childhood-onset 617054
Green Green List (high evidence)
VPS13A
2 reviews
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • Radboud University Medical Center, Nijmegen
  • Illumina TruGenome Clinical Sequencing Services
Phenotypes
  • Choreoacanthocytosis 200150
Green Green List (high evidence)
WDR45
2 reviews
1 green
X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)
Sources
  • Expert Review Green
Phenotypes
  • Neurodegeneration with brain iron accumulation 5 300894
Green Green List (high evidence)
XPR1
2 reviews
1 green
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Other
  • Expert Review Green
Phenotypes
  • Basal ganglia calcification, idiopathic, 6 616413
Amber Amber List (moderate evidence)
GFAP
2 reviews
1 red
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Expert Review Amber
Phenotypes
  • Alexander disease 203450
Red Red List (low evidence)
AIFM1
4 reviews
1 green 1 red
X-LINKED: hemizygous mutation in males, biallelic mutations in females
Sources
  • Expert Review Red
  • Illumina TruGenome Clinical Sequencing Services
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Combined oxidative phosphorylation deficiency 6 300816
Tags
  • watchlist
Red Red List (low evidence)
BDNF
2 reviews
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Emory Genetics Laboratory
  • Expert Review Red
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Central hypoventilation syndrome, congenital 209880
Red Red List (low evidence)
DCAF10
2 reviews
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Red
Red Red List (low evidence)
HEXA
2 reviews
1 red
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Red
Phenotypes
  • GM2-gangliosidosis, several forms 272800
  • Tay-Sachs disease 272800
  • [Hex A pseudodeficiency] 272800 AR
Red Red List (low evidence)
HTT
2 reviews
1 green
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Expert Review Red
Phenotypes
  • Huntington disease 143100
Tags
  • currently-ngs-unreportable
  • nucleotide-repeat-expansion
Red Red List (low evidence)
NDUFA2
3 reviews
1 green 1 red
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Red
Red Red List (low evidence)
NDUFA9
3 reviews
1 green 1 red
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Red
Phenotypes
  • Leigh syndrome due to mitochondrial complex I deficiency 256000
Red Red List (low evidence)
NDUFS3
3 reviews
1 green 1 red
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Red
Phenotypes
  • Leigh syndrome due to mitochondrial complex I deficiency 256000
  • Mitochondrial complex I deficiency 252010
Red Red List (low evidence)
NUP62
2 reviews
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Red
Phenotypes
  • Striatonigral degeneration, infantile 271930
Tags
  • founder-effect
  • watchlist
Red Red List (low evidence)
PDX1
2 reviews
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Red
Phenotypes
  • MODY, type IV 606392
  • Pancreatic agenesis 1 260370
Red Red List (low evidence)
SUOX
2 reviews
1 red
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Red

1 STR

1 reviewed, 0 green

List STR Reviews Mode of inheritance Details
1 STRs
Red Red List (low evidence)
HTT_CAG
1 review
1 green
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert list
Phenotypes
  • Huntington disease 143100
Tags
  • STR

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