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Intracerebral calcification disorders (Version 1.36)

Level 3: Parenchymal brain disorders
Level 2: Neurology and neurodevelopmental disorders

Panel types: Rare Disease 100K
Previous code: 568f8db422c1fc1c79ca1777
Description
This panel is NO LONGER ACTIVELY MAINTAINED.

Please use with caution, as the gene list has not been recently updated. Reviews added to this panel are no longer a priority for curation and may not be followed up.

Please consider using an NHS Genomic Medicine Service (GMS) panel instead. The full list of GMS panels can be found here: https://nhsgms-panelapp.genomicsengland.co.uk/panels, with links back to PanelApp should you wish to leave a review on the panel.

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Intracerebral calcification disorders inclusion criteria (36622)
•	Intracerebral calcification identified on brain imaging in the absence of a known genetic cause.

Intracerebral calcification disorders exclusion criteria (36622)
•	Known genetic diagnosis.
•	Evidence of causative environmental cause, for example infection
•	Phenotype indicative of other recruitable rare disorder, for example Cockayne syndrome

Prior genetic testing guidance (36622)
- 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.

Intracerebral calcification disorders prior genetic testing genes (36622)
Testing of the following genes should be carried out PRIOR TO RECRUITMENT where this is in line with current local practice: 
 -	Guided by phenotype, for example UKGTN Aidcardi-Goutieres syndrome gene panel testing

Closing statement (36622)
These requirements will be kept under continual review during the main programme and may be subject to change.
Panel Activity

12 reviewers

  • Ellen McDonagh (Genomics England Curator)

    Group: Other
    Workplace: Other

  • Richard Scott (Genomics England Curator)

    Group: Other
    Workplace: Other

  • Ellen Thomas (Genomics England Curator)

    Group: Other
    Workplace: Other

  • Yanick Crow (University of Manchester)

    Group: GeCIP domain
    Workplace: Other clinical service

  • Sarah Leigh (Genomics England Curator)

    Group: Other
    Workplace: Other

  • Cristina Dias (The Francis Crick Institute)

    Group: NHS Genomic Medicine Centre
    Workplace: Other

  • Louise Daugherty (Genomics England Curator)

    Group: Other
    Workplace: Other

  • Zornitza Stark (Australian Genomics)

    Group: Other
    Workplace: Other clinical service

  • Anna de Burca (Oxford University Hospitals NHS Foundation Trust)

    Group: NHS Genomic Medicine Centre
    Workplace: NHS clinical service

  • Ivone Leong (Genomics England Curator)

    Group: Other
    Workplace: Other

  • Raquel Real (UCL Queen Square Institute of Neurology)

    Group: GeCIP domain
    Workplace: Research lab

  • Arina Puzriakova (Genomics England Curator)

    Group: Other
    Workplace: Other

33 Entities

33 reviewed, 25 green

List Entity Reviews Mode of inheritance Details
33 Entitiess
Green List (high evidence)
ACP5
2 reviews
1 green 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert list
  • Expert Review Green
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Spondyloenchondrodysplasia with immune dysregulation
  • Spondyloenchondrodysplasia, short stature, SLE, intracranial calcification, spasticity, chilblains, autoimmune haemolytic anaemia
Tags
Green List (high evidence)
ADAR
2 reviews
1 green 		BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Sources
  • Eligibility statement prior genetic testing
  • Expert list
  • Expert Review Green
  • Radboud University Medical Center, Nijmegen
  • UKGTN
Phenotypes
  • Aicardi-Goutieres syndrome 6, OMIM:615010
  • Dyschromatosis symmetrica hereditaria, OMIM:127400
Tags
Green List (high evidence)
AP1S2
2 reviews
 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
Phenotypes
  • Pettigrew syndrome, OMIM:304340
  • Calcifications in basal ganglia
Tags
Green List (high evidence)
COL4A1
2 reviews
1 green 		MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert list
  • Expert Review Green
Phenotypes
  • Porencephaly 1
  • Variable phenotype - porencephaly, destructive cerebral lesions, eye anomalies, intracerebral calcification
Tags
Green List (high evidence)
CTC1
2 reviews
1 green 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert list
  • Expert Review Green
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Cerebroretinal microangiopathy with calcifications and cysts, 612199
  • Coats Plus syndrome
Tags
Green List (high evidence)
CYP2U1
3 reviews
1 green 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert list
  • Expert Review Green
Phenotypes
  • Spastic paraplegia 56, autosomal recessive
Tags
Green List (high evidence)
FARSA
2 reviews
1 red 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • Literature
Phenotypes
  • ?Rajab interstitial lung disease with brain calcifications 2, OMIM:619013
Tags
Green List (high evidence)
FARSB
2 reviews
2 green 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert list
  • Expert Review Green
Phenotypes
  • Rajab syndrome, MIM#613658
  • interstitial lung disease
  • brain calcifications
  • microcephaly
  • intellectual disability
Tags
Green List (high evidence)
IFIH1
2 reviews
1 green 		MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Eligibility statement prior genetic testing
  • Expert list
  • Expert Review Green
  • UKGTN
Phenotypes
  • Aicardi-Goutieres syndrome 7, OMIM:615846
Tags
Green List (high evidence)
JAM3
1 review
 BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Hemorrhagic destruction of the brain, subependymal calcification, and cataracts, 613730
Tags
Green List (high evidence)
KIAA1161
2 reviews
1 green 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • Literature
Phenotypes
  • Primary Familial Brain Calcification
  • Basal ganglia calcification, idiopathic, 7, autosomal recessive, 618317
Tags
  • gene-checked
  • new-gene-name
Green List (high evidence)
NRROS
1 review
1 green 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • Literature
Phenotypes
  • Seizures, early-onset, with neurodegeneration and brain calcification 618875
Tags
Green List (high evidence)
OCLN
2 reviews
1 green 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert list
  • Expert Review Green
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Band-like calcification with simplified gyration and polymicrogyria
  • Band-like calcification with simplified gyration and polymicrogyria, 251290
  • Severe developmental delay with microcephaly
Tags
  • structural-variant
Green List (high evidence)
PDGFB
2 reviews
1 green 		MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Expert list
  • Expert Review Green
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Basal ganglia calcification, idiopathic, 5, 615483
  • Fahr syndrome
Tags
Green List (high evidence)
PDGFRB
2 reviews
1 green 		MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Emory Genetics Laboratory
  • Expert list
  • Expert Review Green
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Basal ganglia calcification idiopathic 4, 615007
  • Calcifications in basal ganglia
  • Fahr syndrome
Tags
Green List (high evidence)
RNASEH2A
2 reviews
1 green 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Eligibility statement prior genetic testing
  • Emory Genetics Laboratory
  • Expert Review Green
  • Illumina TruGenome Clinical Sequencing Services
  • Other
  • UKGTN
Phenotypes
  • Aicardi-Goutieres syndrome 4
  • Aicardi-Goutieres Syndrome
Tags
Green List (high evidence)
RNASEH2B
2 reviews
1 green 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Eligibility statement prior genetic testing
  • Emory Genetics Laboratory
  • Expert Review Green
  • Illumina TruGenome Clinical Sequencing Services
  • Other
  • UKGTN
Phenotypes
  • Aicardi-Goutieres syndrome 2, OMIM:610181
Tags
Green List (high evidence)
RNASEH2C
2 reviews
1 green 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Eligibility statement prior genetic testing
  • Emory Genetics Laboratory
  • Expert Review Green
  • Illumina TruGenome Clinical Sequencing Services
  • Other
  • UKGTN
Phenotypes
  • Aicardi-Goutieres syndrome 3
  • Aicardi-Goutieres Syndrome
Tags
Green List (high evidence)
SAMHD1
2 reviews
1 green 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Eligibility statement prior genetic testing
  • Emory Genetics Laboratory
  • Expert list
  • Expert Review Green
  • Illumina TruGenome Clinical Sequencing Services
  • UKGTN
Phenotypes
  • Aicardi-Goutieres syndrome
  • Aicardi-Goutieres Syndrome
Tags
Green List (high evidence)
SLC20A2
3 reviews
1 green 		MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Expert list
  • Expert Review Green
  • Illumina TruGenome Clinical Sequencing Services
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Basal ganglia calcification, idiopathic, 1, 213600
  • Familial Idiopathic Basal Ganglia Calcification
  • Fahr syndrome
Tags
  • deletions
Green List (high evidence)
TINF2
2 reviews
1 green 		MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert list
  • Expert Review Green
Phenotypes
  • Revesz syndrome, 268130
Tags
Green List (high evidence)
TREM2
1 review
 BIALLELIC, autosomal or pseudoautosomal
Sources
  • Emory Genetics Laboratory
  • Expert Review Green
Phenotypes
  • Calcifications in basal ganglia
  • Nasu-Hakola disease
  • Polycystic lipomembranous osteodysplasia with sclerosing leukoencephalopathy (PLOSL)
Tags
Green List (high evidence)
TREX1
2 reviews
1 green 		BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Sources
  • Eligibility statement prior genetic testing
  • Expert Review Green
  • Illumina TruGenome Clinical Sequencing Services
  • Other
  • UKGTN
Phenotypes
  • Aicardi-Goutieres syndrome 1, dominant and recessive
  • Aicardi-Goutières syndrome, isolated chilblains, lupus-like disease, retinal vasculopathy with cerebral leukodystrophy
Tags
Green List (high evidence)
USP18
1 review
 BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • Literature
Phenotypes
  • pseudo-TORCH syndrome
Tags
Green List (high evidence)
XPR1
2 reviews
1 green 		MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert Review Green
  • Literature
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Basal ganglia calcification (Fahr syndrome)
  • Basal ganglia calcification, idiopathic, 6, 616413
Tags
Red List (low evidence)
ERCC6
2 reviews
 BIALLELIC, autosomal or pseudoautosomal
Sources
  • Emory Genetics Laboratory
  • Expert Review Red
Phenotypes
  • Intercranial Calcifications
Tags
Red List (low evidence)
MAT1A
1 review
 Not set
Sources
  • Emory Genetics Laboratory
  • Expert Review Red
Phenotypes
  • Calcifications in basal ganglia
  • Methionine adenosyltransferase deficiency, autosomal recessive
Tags
Red List (low evidence)
PCDH12
2 reviews
2 red 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review
Phenotypes
  • intellectual disability
  • microcephaly
  • epilepsy
  • perithalamic hyperechogenicity
  • periventricular hyperechogenicity
  • midbrain abnormalities
  • hypothalamic abnormalities
Tags
  • founder-effect
Red List (low evidence)
SCN2A
1 review
1 red 		MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Literature
Phenotypes
  • Epileptic encephalopathy, early infantile, 11
  • Seizures, benign familial infantile, 3
Tags
Red List (low evidence)
SNORD118
2 reviews
 BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert list
Phenotypes
  • 614561
Tags
  • locus-type-small-nucleolar
No list
JAM2
1 review
1 green 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Literature
Phenotypes
  • Primary brain calcification
Tags
No list
RNASET2
1 review
1 green 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert list
Phenotypes
  • Leukoencephalopathy, cystic, without megalencephaly, MIM# 612951
Tags
No list
TYROBP
1 review
1 green 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert list
Phenotypes
  • Polycystic lipomembranous osteodysplasia with sclerosing leukoencephalopathy 1, MIM# 221770
Tags

Major version comments

  • 19th Dec 2016: panel revised according to expert review and internal curation review.

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Download lists

  • Whole panel
  • Green list (high evidence)
  • Green and Amber Genes
  • Amber Genes
  • Red list (low evidence)

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