Structural basal ganglia disorders (Version 1.39)

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.

Panel Activity

8 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: Other
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
Arina Puzriakova (Genomics England Curator)

Group: Other
Workplace: Other

77 Entities

77 reviewed, 64 green

List	Entity	Reviews	Mode of inheritance	Details
Filter Entities 77 Entitiess
Green Green List (high evidence)	ADAR	2 reviews 1 green	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Green Literature Phenotypes Aicardi-Goutieres syndrome 6, OMIM:615010 Tags
Green Green List (high evidence)	AP1S2	3 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 Emory Genetics Laboratory Expert Review Green Radboud University Medical Center, Nijmegen Phenotypes Pettigrew syndrome, OMIM:304340 Tags
Green Green List (high evidence)	ATP13A2	2 reviews 1 green	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Green Literature Phenotypes Kufor-Rakeb syndrome 606693 Tags
Green Green List (high evidence)	ATP7B	2 reviews 1 green	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Green Literature Phenotypes Wilson disease 277900 Tags
Green Green List (high evidence)	BCS1L	3 reviews 3 green	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Green Literature Tags
Green Green List (high evidence)	C19orf12	3 reviews 2 green	BOTH monoallelic and biallelic, autosomal or pseudoautosomal	Sources Expert Review Green Literature Phenotypes ?Spastic paraplegia 43, autosomal recessive, OMIM:615043 Neurodegeneration with brain iron accumulation 4, OMIM: 614298 Tags
Green Green List (high evidence)	COASY	2 reviews 1 green	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Green Literature Phenotypes Neurodegeneration with brain iron accumulation 6, OMIM:615643 neurodegeneration with brain iron accumulation 6, MONDO:0014290 Tags
Green Green List (high evidence)	COX10	4 reviews 2 green 1 red	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Green Literature Phenotypes Mitochondrial complex IV deficiency, nuclear type 3, OMIM:619046 Tags
Green Green List (high evidence)	COX15	4 reviews 3 green	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Green Literature Phenotypes Mitochondrial complex IV deficiency, nuclear type 6, OMIM:615119 Tags
Green Green List (high evidence)	CP	2 reviews 1 green	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Green Literature Phenotypes Cerebellar ataxia 604290 Hemosiderosis, systemic, due to aceruloplasminemia 604290 [Hypoceruloplasminemia, hereditary] 604290 Tags
Green Green List (high evidence)	DLAT	5 reviews 3 green	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Green Literature Phenotypes Pyruvate dehydrogenase E2 deficiency 245348 Tags
Green Green List (high evidence)	ETHE1	4 reviews 2 green	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Green Literature Phenotypes Ethylmalonic encephalopathy 602473 Tags
Green Green List (high evidence)	FA2H	2 reviews 1 green	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Green Literature Phenotypes Spastic paraplegia 35, autosomal recessive 612319 Tags
Green Green List (high evidence)	FOXP2	2 reviews 1 green	MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted	Sources Emory Genetics Laboratory Expert Review Green Illumina TruGenome Clinical Sequencing Services Radboud University Medical Center, Nijmegen Phenotypes Speech-language disorder-1 602081 Tags
Green Green List (high evidence)	FTL	1 review 1 green	MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted	Sources Illumina TruGenome Clinical Sequencing Services Radboud University Medical Center, Nijmegen UKGTN Phenotypes Neurodegeneration with brain iron accumulation 3 606159 Tags
Green Green List (high evidence)	GCDH	2 reviews 1 green	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Green Literature Tags
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 Tags
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, OMIM:615846 Tags
Green Green List (high evidence)	ISG15	2 reviews 1 red	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Green Other Phenotypes Immunodeficiency 38 616126 Tags
Green Green List (high evidence)	IVD	2 reviews 1 green	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Green Literature Phenotypes Isovaleric acidemia 243500 Tags
Green Green List (high evidence)	KIAA1161	1 review 1 green	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Expert Review Green Phenotypes Autosomal Recessive Primary Familial Brain Calcification Basal ganglia calcification, idiopathic, 7, autosomal recessive Calcifications in the basal ganglia Tags gene-checked new-gene-name
Green Green List (high evidence)	KMT2B	2 reviews 1 green	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Expert Review Green Literature Phenotypes Dystonia 28, childhood-onset, OMIM:617284 early-onset dystonia Tags treatable
Green Green List (high evidence)	MECR	2 reviews 1 green	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Green Literature Phenotypes Dystonia, childhood-onset, with optic atrophy and basal ganglia abnormalities 617282 Tags
Green Green List (high evidence)	MT-ATP6	4 reviews 2 green 1 red	MITOCHONDRIAL	Sources Expert Review Green Literature Tags gene-checked
Green Green List (high evidence)	MT-ND1	5 reviews 3 green	MITOCHONDRIAL	Sources Expert Review Green Literature Tags gene-checked
Green Green List (high evidence)	MT-ND6	5 reviews 3 green	MITOCHONDRIAL	Sources Expert Review Green Literature Tags gene-checked
Green Green List (high evidence)	MUT	3 reviews 1 green	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Green Literature Phenotypes Methylmalonic aciduria, mut(0) type 251000 Tags new-gene-name
Green Green List (high evidence)	NDUFA1	4 reviews 1 green 1 red	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 Literature Phenotypes Mitochondrial complex I deficiency 252010 Tags
Green Green List (high evidence)	NDUFA10	3 reviews 2 green	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Green Literature Phenotypes Leigh syndrome 256000 Tags
Green Green List (high evidence)	NDUFAF2	4 reviews 1 green 1 red	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Green Literature Tags
Green Green List (high evidence)	NDUFAF6	3 reviews 2 green	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Green Literature Phenotypes Leigh syndrome due to mitochondrial complex I deficiency 256000 Tags
Green Green List (high evidence)	NDUFS4	3 reviews 2 green	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Green Literature Phenotypes Leigh syndrome 256000 Mitochondrial complex I deficiency 252010 Tags
Green Green List (high evidence)	NDUFS7	3 reviews 1 green 1 red	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Green Literature Tags
Green Green List (high evidence)	NDUFS8	3 reviews 2 green	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Green Literature Tags
Green Green List (high evidence)	NDUFV1	3 reviews 1 green 1 red	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Green Literature Tags
Green Green List (high evidence)	OCLN	2 reviews 1 green	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Green Radboud University Medical Center, Nijmegen UKGTN Phenotypes Band-like calcification with simplified gyration and polymicrogyria 251290 Tags
Green Green List (high evidence)	PANK2	3 reviews 3 green	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Expert Review Green Tags
Green Green List (high evidence)	PCCA	2 reviews 1 green	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Green Literature Phenotypes Propionicacidemia 606054 Tags
Green Green List (high evidence)	PCCB	2 reviews 1 green	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Green Literature Phenotypes Propionicacidemia 606054 Tags
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 Tags
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 Tags
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 Tags
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 Emory Genetics Laboratory Expert Review Green Radboud University Medical Center, Nijmegen Phenotypes Pyruvate dehydrogenase E1-alpha deficiency 312170 Tags
Green Green List (high evidence)	PDP1	5 reviews 3 green	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Green Literature Phenotypes Pyruvate dehydrogenase phosphatase deficiency, 608782 Tags
Green Green List (high evidence)	PLA2G6	2 reviews 1 green	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Green Literature Phenotypes Infantile neuroaxonal dystrophy 1 256600 Neurodegeneration with brain iron accumulation 2B 610217 Parkinson disease 14, autosomal recessive 612953 Tags
Green Green List (high evidence)	PRNP	1 review 1 green	MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted	Sources Illumina TruGenome Clinical Sequencing Services Radboud University Medical Center, Nijmegen UKGTN Phenotypes Cerebral amyloid angiopathy, PRNP-related 137440 Gerstmann-Straussler disease 137440 Huntington disease-like 1 603218 Creutzfeldt-Jakob disease 123400 Tags
Green Green List (high evidence)	RAB39B	2 reviews 1 red	X-LINKED: hemizygous mutation in males, biallelic mutations in females	Sources Emory Genetics Laboratory Expert Review Green Phenotypes Waisman syndrome 311510 Tags
Green Green List (high evidence)	SDHA	3 reviews 2 green	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Green Literature Tags
Green Green List (high evidence)	SERAC1	4 reviews 2 green	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Green Literature Phenotypes 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome, OMIM:614739 Lesions in the basal ganglia Tags
Green Green List (high evidence)	SLC19A3	4 reviews 3 green	BIALLELIC, autosomal or pseudoautosomal	Sources Emory Genetics Laboratory Illumina TruGenome Clinical Sequencing Services Radboud University Medical Center, Nijmegen UKGTN Phenotypes Thiamine metabolism dysfunction syndrome 2 (biotin- or thiamine-responsive encephalopathy type 2) 607483 Tags
Green Green List (high evidence)	SLC20A2	1 review 1 green	MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted	Sources Emory Genetics Laboratory Illumina TruGenome Clinical Sequencing Services Radboud University Medical Center, Nijmegen Phenotypes Basal ganglia calcification, idiopathic, 1 213600 Tags
Green Green List (high evidence)	SLC25A19	5 reviews 3 green	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Green Literature Phenotypes Microcephaly, Amish type 607196 Thiamine metabolism dysfunction syndrome 4 (progressive polyneuropathy type) 613710 Tags
Green Green List (high evidence)	SLC30A10	2 reviews 1 green	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Green Literature Phenotypes Hypermanganesemia with dystonia 1, OMIM:613280 Tags treatable
Green Green List (high evidence)	SLC39A14	2 reviews 1 green	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Green Literature 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 Literature Phenotypes Mitochondrial DNA depletion syndrome 5 (encephalomyopathic with or without methylmalonic aciduria), OMIM:612073 Tags
Green Green List (high evidence)	SUCLG1	3 reviews 3 green	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Green Literature Tags
Green Green List (high evidence)	SURF1	4 reviews 3 green	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Green Literature Tags
Green Green List (high evidence)	TOR1A	1 review 1 green	MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted	Sources Emory Genetics Laboratory Illumina TruGenome Clinical Sequencing Services Radboud University Medical Center, Nijmegen UKGTN Phenotypes Dystonia-1, torsion, OMIM:128100 Dystonic disorder, MONDO:0003441 Tags
Green Green List (high evidence)	TUBA1A	1 review	MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted	Sources Emory Genetics Laboratory Illumina TruGenome Clinical Sequencing Services Radboud University Medical Center, Nijmegen UKGTN Phenotypes Lissencephaly 3 611603 Tags
Green Green List (high evidence)	TUBB4A	2 reviews 1 green	MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted	Sources Expert Review Green Illumina TruGenome Clinical Sequencing Services Radboud University Medical Center, Nijmegen Phenotypes Leukodystrophy, hypomyelinating, 6 612438 Tags
Green Green List (high evidence)	VAC14	2 reviews 1 green	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Green Literature Phenotypes Striatonigral degeneration, childhood-onset 617054 Tags
Green Green List (high evidence)	VPS13A	2 reviews 1 green	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Green Illumina TruGenome Clinical Sequencing Services Radboud University Medical Center, Nijmegen Phenotypes Choreoacanthocytosis 200150 Tags
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 Literature Phenotypes Neurodegeneration with brain iron accumulation 5 300894 Tags
Green Green List (high evidence)	XPR1	2 reviews 1 green	MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted	Sources Expert Review Green Other Phenotypes Basal ganglia calcification, idiopathic, 6 616413 Tags
Amber Amber List (moderate evidence)	GFAP	2 reviews 1 red	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Expert Review Amber Literature Phenotypes Alexander disease 203450 Tags
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 Tags
Red Red List (low evidence)	DCAF10	2 reviews 1 green	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Red Literature Tags
Red Red List (low evidence)	HEXA	2 reviews 1 red	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Red Literature Phenotypes GM2-gangliosidosis, several forms 272800 Tay-Sachs disease 272800 [Hex A pseudodeficiency] 272800 AR Tags
Red Red List (low evidence)	HTT	3 reviews 1 green	Other	Sources Expert Review Red Literature Phenotypes Huntington disease, OMIM: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 Literature Tags
Red Red List (low evidence)	NDUFA9	3 reviews 1 green 1 red	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Red Literature Phenotypes Leigh syndrome due to mitochondrial complex I deficiency 256000 Tags
Red Red List (low evidence)	NDUFS3	3 reviews 1 green 1 red	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Red Literature Phenotypes Leigh syndrome due to mitochondrial complex I deficiency 256000 Mitochondrial complex I deficiency 252010 Tags
Red Red List (low evidence)	NUP62	2 reviews 1 green	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Red Literature 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 Literature Phenotypes MODY, type IV 606392 Pancreatic agenesis 1 260370 Tags
Red Red List (low evidence)	SUOX	2 reviews 1 red	BIALLELIC, autosomal or pseudoautosomal	Sources Expert Review Red Literature Tags
No list No list	HTT_CAG STR	3 reviews 1 green	MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted	Sources Expert list Expert Review Removed NHS GMS Phenotypes Huntington disease, OMIM:143100 Tags curated_removed STR

Structural basal ganglia disorders (Version 1.39)

8 reviewers

77 Entities

77 reviewed, 64 green

2 reviews

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