SURF1-Related Leigh Syndrome (LS) via the SURF1 Gene
- Summary and Pricing
- Clinical Features and Genetics
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In the general population, pathogenic variation in the SURF1 gene is one of the most frequent causes of LS associated with cytochrome c oxidase (COX) deficiency (Tiranti et al. 1998; Zhu et al. 1998). One large cohort study was complicated by the presence of a founder mutation in the affected population, resulting in a high prevalence of SURF1-related LS that is likely not representative of the general population (Böhm et al. 2006). Analytical sensitivity of this test is expected to be high, however, as the majority of documented pathogenic variants in SURF1 are detectable by this sequencing test.
Leigh Syndrome (LS), also known as subacute necrotizing encephalomyelopathy, is a severe neurodegenerative disorder resulting primarily from defects in the mitochondrial respiratory chain (Ruhoy and Saneto 2014; Zhu et al. 1998; Leigh 1951). The disease incidence for LS is estimated to be around 1:32,000 to 1:40,000 live births (Darin et al. 2001; Rahman et al. 1996).
The hallmark features that characterize this syndrome include elevated levels of lactate in blood and cerebral spinal fluid, and the presence of bilateral symmetric necrotic lesions in the basal ganglia, brain stem, thalamus, and/or spinal cord (Wedatilake et al. 2013; Leigh 1951). Patients also present with isolated or combined mitochondrial complex deficiencies, psychomotor delay or regression, and neurologic manifestations such as hypotonia or ataxia. The term ‘Leigh-Like Syndrome (LLS)’ is used to describe a similar clinical presentation in which one or more of these diagnostic characteristics is atypical.
Symptomatic onset of this disorder usually occurs shortly after birth or within the first three years of life, although cases of adult-onset LS/LLS have been reported (Ronchi et al. 2011). LS/LLS infants often present with feeding difficulties, gastrointestinal distress, hypotonia, and growth delays, while older children (>1 years) may develop additional symptoms including developmental regression (loss of cognitive or motor skills), dysphagia, hypertrichosis, dystonic posturing, nystagmus, and opthalmoplegia (Wedatilake et al. 2013).
LS and LLS have been linked to pathogenic variants in over 60 different genes (Rahman 2015). However, while defects in certain genes are more likely to result in classic LS rather than atypical LLS, genotype-phenotype correlations are still poorly understood. In the general population, pathogenic variation in the SURF1 gene is one of the most frequent causes of LS associated with cytochrome c oxidase (COX) deficiency (Tiranti et al. 1998; Zhu et al. 1998).
Leigh and Leigh-Like Syndromes (LS/LLS) are caused by defects in the mitochondrial oxidative phosphorylation (OXPHOS) complexes or associated proteins, such as OXPHOS assembly factors or the pyruvate dehydrogenase (PDH) complex (for a review, see Rahman 2015). As a result, the LS/LLS phenotypes exhibit significant genetic heterogeneity, and pathogenic variants in over 60 different genes have been reported to be causative for this disorder. Depending on the cellular localization of the affected gene(s), these syndromes may be inherited in an autosomal recessive, maternal, or X-linked recessive manner.
Nuclear genes associated with autosomal recessive inheritance of LS/LLS include: SURF1, BCS1L, C12ORF65, COX10, COX15, FOXRED1, GFM1, LRPPRC, NDUFA2, NDUFA4, NDUFA9, NDUFA10, NDUFA11, NDUFA12, NDUFAF2, NDUFAF5, NDUFAF6, NDUFS1, NDUFS2, NDUFS3, NDUFS4, NDUFS7, NDUFS8, NDUFV1, PDSS2, PET100, SCO2, SDHA, SDHAF1, SLC19A3, SUCLA2, SUCLG1, TACO1, TTC19, UQCRQ, SERAC1, NDUFV2, MTFMT, HIBCH, TSFM, ECHS1, LIAS, PNPT1, POLG, LIPT1, DLD, TPK1, and ETHE1.
Mitochondrial genes associated with maternal inheritance of LS/LLS include: MT-ATP6, MT-TL1, MT-TK, MT-TW, MT-TV, MT-ND1, MT-ND2, MT-ND3, MT-ND4, MT-ND5, MT-ND6, and MT-CO3 .
X-linked genes associated with X-linked recessive inheritance of LS/LLS include: NDUFA1, AIFM1, PDHA1, PDHB, and PDHX. In this form of inheritance, male patients are more frequently affected, although heterozygous females may present with LS/LLS due to skewed X-inactivation (Patel et al. 2012).
The SURF1 gene, comprised of nine exons, is thought to encode for an assembly or maintenance factor for the cytochrome c oxidase (COX/complex IV) (Zhu et al. 1998; Tiranti et al. 1999). A number of pathogenic variants (>80) have been documented for SURF1-associated autosomal recessive LS, although the majority of identified mutations cluster within exons 6-8 (for a review, see Wedatilake et al. 2013). Deletions and/or insertions of one or more nucleotides are a common cause of SURF1 gene disruption, usually resulting in frameshifts and premature protein termination. A number of missense mutations, some of which abolish existing splice sites, have also been reported, in addition to several duplication events (Tiranti et al. 1998; Wedatilake et al. 2013). One small deletion (c.845_846delCT) is prevalent among patients with Slavic ancestry (Böhm et al. 2006).
Full gene sequencing of SURF1 is performed, with bidirectional sequencing of exons 1-9. The full coding region of each exon plus ~10 bp of flanking non-coding DNA on either side are sequenced. We will also sequence any single exon (Test #100) or pair of exons (Test #200) in family members of patients with known mutations or to confirm research results.
Indications for Test
SURF1 sequencing should be considered in patients with a family history of LS or childhood encephalopathy, or patients who present with symptoms consistent with LS. We will also sequence the SURF1 gene to determine carrier status.
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- Böhm M et al. 2006. Pediatric Research. 59: 21-6. PubMed ID: 16326995
- Darin N. et al. 2001. Annals of Neurology. 49: 377-83. PubMed ID: 11261513
- Leigh D. 1951. Journal of Neurology, Neurosurgery, and Psychiatry. 14: 216-21. PubMed ID: 14874135
- Patel K. et al. 2012. Molecular Genetics and Metabolism. 105: 34-43. PubMed ID: 22079328
- Rahman S. 2015. Nuclear Gene-Encoded Leigh Syndrome Overview. In: Pagon RA, Adam MP, Bird TD, Dolan CR, Fong C-T, Smith RJ, and Stephens K, editors. GeneReviews(®), Seattle (WA): University of Washington, Seattle. PubMed ID: 26425749
- Rahman S. et al. 1996. Annals of Neurology. 39:343-51. PubMed ID: 8602753
- Ronchi D. et al. 2011. Biochemical and Biophysical Research Communications. 412: 245-8. PubMed ID: 21819970
- Ruhoy IS. and Saneto RP. 2014. The Application of Clinical Genetics. 7: 221-34. PubMed ID: 25419155
- Tiranti V. et al. 1998. American Journal of Human Genetics. 63: 1609-21. PubMed ID: 9837813
- Tiranti V. et al. 1999. Human Molecular Genetics. 8: 2533-40. PubMed ID: 10556302
- Wedatilake Y. et al. 2013. Orphanet Journal of Rare Diseases. 8: 96. PubMed ID: 23829769
- Zhu Z. et al. 1998. Nature Genetics. 20: 337-43. PubMed ID: 9843204
Bi-Directional Sanger Sequencing
Nomenclature for sequence variants was from the Human Genome Variation Society (http://www.hgvs.org). As required, DNA is extracted from the patient specimen. PCR is used to amplify the indicated exons plus additional flanking non-coding sequence. After cleaning of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit. Products are resolved by electrophoresis on an ABI 3730xl capillary sequencer. In most cases, sequencing is performed in both forward and reverse directions; in some cases, sequencing is performed twice in either the forward or reverse directions. In nearly all cases, the full coding region of each exon as well as 10 bases of non-coding DNA flanking the exon are sequenced.
As of February 2018, we compared 26.8 Mb of Sanger DNA sequence generated at PreventionGenetics to NextGen sequence generated in other labs. We detected only 4 errors in our Sanger sequences, and these were all due to allele dropout during PCR. For Proficiency Testing, both external and internal, in the 14 years of our lab operation we have Sanger sequenced roughly 14,300 PCR amplicons. Only one error has been identified, and this was an error in analysis of sequence data.
Our Sanger sequencing is capable of detecting virtually all nucleotide substitutions within the PCR amplicons. Similarly, we detect essentially all heterozygous or homozygous deletions within the amplicons. Homozygous deletions which overlap one or more PCR primer annealing sites are detectable as PCR failure. Heterozygous deletions which overlap one or more PCR primer annealing sites are usually not detected (see Analytical Limitations). All heterozygous insertions within the amplicons up to about 100 nucleotides in length appear to be detectable. Larger heterozygous insertions may not be detected. All homozygous insertions within the amplicons up to about 300 nucleotides in length appear to be detectable. Larger homozygous insertions may masquerade as homozygous deletions (PCR failure).
In exons where our sequencing did not reveal any variation between the two alleles, we cannot be certain that we were able to PCR amplify both of the patient’s alleles. Occasionally, a patient may carry an allele which does not amplify, due for example to a deletion or a large insertion. In these cases, the report contains no information about the second allele.
Similarly, our sequencing tests have almost no power to detect duplications, triplications, etc. of the gene sequences.
In most cases, only the indicated exons and roughly 10 bp of flanking non-coding sequence on each side are analyzed. Test reports contain little or no information about other portions of the gene, including many regulatory regions.
In nearly all cases, we are unable to determine the phase of sequence variants. In particular, when we find two likely causative mutations for recessive disorders, we cannot be certain that the mutations are on different alleles.
Our ability to detect minor sequence variants, due for example to somatic mosaicism is limited. Sequence variants that are present in less than 50% of the patient’s nucleated cells may not be detected.
Runs of mononucleotide repeats (eg (A)n or (T)n) with n >8 in the reference sequence are generally not analyzed because of strand slippage during PCR and cycle sequencing.
Unless otherwise indicated, the sequence data that we report are based on DNA isolated from a specific tissue (usually leukocytes). Test reports contain no information about gene sequences in other tissues.
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- Collect 3 ml -5 ml (5 ml preferred) of whole blood in EDTA (purple top tube) or ACD (yellow top tube). For Test #500-DNA Banking only, collect 10 ml -20 ml of whole blood.
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- Send in screw cap tube at least 5 µg -10 µg of purified DNA at a concentration of at least 20 µg/ml for NGS and Sanger tests and at least 5 µg of purified DNA at a concentration of at least 100 µg/ml for gene-centric aCGH, MLPA, and CMA tests, minimum 2 µg for limited specimens.
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