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Biotin-Thiamine-Responsive Basal Ganglia Disease via the SLC19A3 Gene

Summary and Pricing

Test Method

Sequencing and CNV Detection via NextGen Sequencing using PG-Select Capture Probes
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
SLC19A3 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
4235SLC19A381479 81479,81479 $990 Order Options and Pricing

Pricing Comments

Testing run on PG-select capture probes includes CNV analysis for the gene(s) on the panel but does not permit the optional add on of exome-wide CNV analysis. Any of the NGS platforms allow reflex to other clinically relevant genes, up to whole exome or whole genome sequencing depending upon the base platform selected for the initial test.

An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.

This test is also offered via a custom panel (click here) on our exome or genome backbone which permits the optional add on of exome-wide CNV or genome-wide SV analysis.

Turnaround Time

3 weeks on average for standard orders or 2 weeks on average for STAT orders.

Please note: Once the testing process begins, an Estimated Report Date (ERD) range will be displayed in the portal. This is the most accurate prediction of when your report will be complete and may differ from the average TAT published on our website. About 85% of our tests will be reported within or before the ERD range. We will notify you of significant delays or holds which will impact the ERD. Learn more about turnaround times here.

Targeted Testing

For ordering sequencing of targeted known variants, go to our Targeted Variants page.


Genetic Counselors


  • Li Fan, MD, PhD, FCCMG, FACMG

Clinical Features and Genetics

Clinical Features

Biotin-thiamine-responsive basal ganglia disease (BTBGD) is a neurological disorder characterized by encephalopathy and neurological decline. BTBGD represents a clinical spectrum of disorders resulting from loss of the neuronal thiamine transporter hTHTR2. Disease onset can occur anytime between infancy and adulthood, with the preponderance of cases showing childhood onset. The first symptoms are often seen following febrile illness or mild trauma and include: subacute episodes of encephalopathy, seizures, ataxia, and/or confusion (Alfadhel et al. 2013; Tabarki et al. 2013). At onset, seizures are generally well controlled with medication. Additional variable symptoms include dystonia, dysarthria, dysphagia, somnolence, external ophthalmoplegia, quadriparesis, and hyperreflexia. If left untreated, severe neurodegeneration is seen, ultimately leading to severe intellectual disability, coma, respiratory insufficiency, and death. In severe cases of BTBGD, patients present during infancy with hypotonia or hyptertonia, difficulty feeding, infantile spasms, and severe psychomotor delay (Kevelam et al. 2013). In these reported cases, EEG readings showed mutlifocal spikes without hypsarrhythmia. Not only is there high phenotypic variability among patients with different SLC19A3 variants, but there can also be considerable variability in disease onset within members of the same family (Alfadhel et al. 2013).

MRI findings reveal bilateral hyperintensity of the basal ganglia (caudate nucleus and putamen) on T2-weighted sequences. Vasogenic edema is also seen on MRI during acute neurometabolic crisis. Involvement of the brain stem and cerebellar cortex and vermis has also been reported (Distelmaier et al. 2013). As the disease progresses, MRI reveals significant brain atrophy and bilateral lesions in the thalami and basal ganglia (Kevelam et al. 2013).

BTBGD is often misdiagnosed as Leigh syndrome as it shares many symptoms with this mitochondrial disorder. BTBGD patients may have lactic acidemia and a lactate peak on magnetic resonance spectroscopy, which further supports a diagnosis of Leigh syndrome (Gerards et al. 2013). However, metabolic screening in BTBGD patients is normal and there is no evidence of respiratory chain deficiency (Debs et al. 2010; Serrano et al. 2012). In addition, MRI in BTBGD patients may show vasogenic edema and diffuse cortical and subcortical changes that are not typical of Leigh syndrome (Distelmaier et al. 2013).

The BTBGD phenotype has also been likened to Wernicke's encephalopathy (WE), thiamine deficiency described in alcoholics, due to the presence of ophthalmoplegia, ataxia, and confusion.

Treatment with a high dose of biotin and additional thiamine has been shown to be effective in BTBGD patients (Tabarki et al. 2013). Patients treated shortly after onset of symptoms showed partial to complete improvement within days, whereas patients treated later into disease progression did not show a complete reversal of symptoms, but did exhibit marked improvement (Alfadhel et al. 2013). Continuous biotin-thiamine therapy is required; symptoms recur upon removal of treatment.


BTBGD is inherited in an autosomal recessive manner and is caused by pathogenic variants in the SLC19A3 gene. Pathogenic nonsense, missense, frameshift, and splice site variants in the SLC19A3 gene have been reported (Debs et al. 2010; Kevelam et al. 2013). Currently there is no clear genotype-phenotype correlation to explain why some patients with pathogenic SLC19A3 variants show a more severe course of disease than others.

SLC19A3 encodes hTHTR2, one of two thiamine transporters localized to the plasma membrane (Gerards et al. 2013). hTHTR2 is a high-affinity low capacity transporter that is expressed in neurons. Once thiamine is imported into the cell it is converted to its active form thiamine pyrophosphate, which is a cofactor for a range of enzymatic reactions.

Combined treatment with biotin and thiamine reverses disease progression in BTBGD patients with pathogenic missense and loss-of-function variants (Haack et al. 2014; Alfadhel et al. 2013). Biotin is not a known substrate of hTHTR2 and the molecular mechanism by which treatment with biotin helps compensate for defective thiamine transport is unclear.

Clinical Sensitivity - Sequencing with CNV PG-Select

Biotin-thiamine-responsive basal ganglia disease is a rare disorder, and clinical sensitivity cannot yet be estimated. Analytical sensitivity should be high because the great majority of pathogenic variants thus far reported are detectable by sequencing genomic DNA.

Testing Strategy

This test provides full coverage of all coding exons of the SLC19A3 gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.

Indications for Test

SLC19A3 sequencing should be considered in patients with symptoms of BTBGD and in patients diagnosed with Leigh syndrome, but for which no impairment of mitochondrial metabolism was detected. SLC19A3 testing is also warranted in patients with childhood encephalopathy that responded to treatment with biotin and thiamine. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in SLC19A3.


Official Gene Symbol OMIM ID
SLC19A3 606152
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Basal Ganglia Disease, Biotin-Responsive AR 607483

Related Test

Leigh and Leigh-Like Syndrome Panel (Nuclear Genes Only)


  • Alfadhel M, Almuntashri M, Jadah RH, Bashiri FA, Rifai MT Al, Shalaan H Al, Balwi M Al, Rumayan A Al, Eyaid W, Al-Twaijri W. 2013. Biotin-responsive basal ganglia disease should be renamed biotin-thiamine-responsive basal ganglia disease: a retrospective review of the clinical, radiological and molecular findings of 18 new cases. Orphanet J Rare Dis 8: 83. PubMed ID: 23742248
  • Debs R, Depienne C, Rastetter A, Bellanger A, Degos B, Galanaud D, Keren B, Lyon-Caen O, Brice A, Sedel F. 2010. Biotin-responsive basal ganglia disease in ethnic Europeans with novel SLC19A3 mutations. Archives of neurology 67: 126–130. PubMed ID: 20065143
  • Distelmaier F, Huppke P, Pieperhoff P, Amunts K, Schaper J, Morava E, Mayatepek E, Kohlhase J, Karenfort M. 2013. Biotin-Responsive Basal Ganglia Disease: A Treatable Differential Diagnosis of Leigh Syndrome. In: Zschocke J, Gibson KM, Brown G, Morava E, and Peters V, editors. JIMD Reports - Case and Research Reports, Volume 13, Berlin, Heidelberg: Springer Berlin Heidelberg, p 53–57. PubMed ID: 24166474
  • Gerards M, Kamps R, Oevelen J van, Boesten I, Jongen E, Koning B de, Scholte HR, Angst I de, Schoonderwoerd K, Sefiani A, Ratbi I, Coppieters W, Karim L, de Coo R, van den Bosch B, Smeets H. 2013. Exome sequencing reveals a novel Moroccan founder mutation in SLC19A3 as a new cause of early-childhood fatal Leigh syndrome. Brain 136: 882–890. PubMed ID: 23423671
  • Haack TB, Klee D, Strom TM, Mayatepek E, Meitinger T, Prokisch H, Distelmaier F. 2014. Infantile Leigh-like syndrome caused by SLC19A3 mutations is a treatable disease. Brain 137: e295–e295. PubMed ID: 24878502
  • Kevelam SH, Bugiani M, Salomons GS, Feigenbaum A, Blaser S, Prasad C, Haberle J, Baric I, Bakker IMC, Postma NL, Kanhai WA, Wolf NI, Abbink TE, Waisfisz Q, Heutink P, van der Knaap MS. 2013. Exome sequencing reveals mutated SLC19A3 in patients with an early-infantile, lethal encephalopathy. Brain 136: 1534–1543. PubMed ID: 23482991
  • Serrano M, Rebollo M, Depienne C, Rastetter A, Fernández-Álvarez E, Muchart J, Martorell L, Artuch R, Obeso JA, Pérez-Dueñas B. 2012. Reversible generalized dystonia and encephalopathy from thiamine transporter 2 deficiency. Movement Disorders 27: 1295–1298. PubMed ID: 22777947
  • Tabarki B, Al-Shafi S, Al-Shahwan S, Azmat Z, Al-Hashem A, Al-Adwani N, Biary N, Al-Zawahmah M, Khan S, Zuccoli G. 2013. Biotin-responsive basal ganglia disease revisited: Clinical, radiologic, and genetic findings. Neurology 80: 261–267. PubMed ID: 23269594


Ordering Options

We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.

myPrevent - Online Ordering

  • The test can be added to your online orders in the Summary and Pricing section.
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For Requisition Forms, visit our Forms page

If ordering a Duo or Trio test, the proband and all comparator samples are required to initiate testing. If we do not receive all required samples for the test ordered within 21 days, we will convert the order to the most effective testing strategy with the samples available. Prior authorization and/or billing in place may be impacted by a change in test code.

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