Friday, August 19, 2016

Genetic teasers

1) A 19 month old girl has a clinical and radiographic course consistent with Joubert syndrome.  Molecular genetic testing shows her heterozygous for a ANKS6 gene sequence variant c.532G>A, resulting in the amino acid substitution p.Glu178Lys.  Prediction programs suggest this is benign, however functional and genetic evidence is deemed inconclusive.  She is also heterozygous in the TMEM67 gene for an intronic variant c.1289-7A>G.   The c.1289-7A>G variant may activate a cryptic AG acceptor site and interfere with normal splicing.  If this new acceptor site is used, it is predicted to result in an in-frame insertion of two amino acids.  In neither case was a second pathogenic mutation identified.

2) An almost 19 year old male has a progressive spastic paraparesis.  Genetic testing identified a p.Ala510Val mutation in the SPG7 paraplegia gene.  No second pathogenic mutation identified. SPG7 mutational screening in spastic paraplegia patients supports a dominant effect for some mutations and a pathogenic role for p.A510V. It describes 4 patients who had a similar kind of mutation and developed symptoms at age 47, 1 year, 44, and 50 years of age. These patients were carrier of only 1 mutation. The SPG7 A510V was found in 8 patients (one was homozygous and 3 were controls). The paper states that these findings suggested some SPG7 mutations could be associated with variable penetrance.

The p.Ala510Val mutation in the SPG7 (paraplegin) gene is the most common mutation causing adult onset neurogenetic disease in patients of British ancestry ( J. Neurol 2013, 260: 1286-1294).  Based on review of this paper, the paper states that the change in the SPG7 was first described as a polymorphism in 1988. This was based on the frequency of 3 to 4% in 2 separate controls in the United Kingdom.

3) An 18 year old male with epilepsy has a MRI showing a linear band of T2-FLAIR hyperintense signal radiating from the subcortical white matter of the left posterior-superior temporal gyrus down  towards the atrium of the left lateral ventricle. In addition, perhaps three subependymal modules were identified. There was also a tiny, linear focus of T2-FLAIR hyperintense signal extending from the right midfrontal cortex down towards the right lateral ventricle.  These findings were deemed relatively mild intracranial stigmata of tuberous sclerosis.

Genetic testing revealed a sequence variant in the TSC1 gene at nucleotide position 2196 (T>C). This was deemed to be a variant of unknown significance. This variant was not predicted to change the amino acid sequence of the protein unless splicing might be affected. This was not a variant that had been identified in other index cases at Athena Diagnostics. Five splicing algorithms were used to analyze thepossible effect of this variant on splicing. None of the five algorithms predicted the elimination of a known splice site. Accordingly, data was generated to suggest that this variant may be more likely benign than pathogenic.


  1. Regarding 2 in the post. The patient subsequently had whole exome sequencing with no abnormality found.

  2. This is a revision of a comment originally posted on October 5, 2016 at 11:56 am


    The patient who inspired this post is heterozygous for a novel variant in the CHD2 gene (c.362 G>T,pArg121Leu). This variant was not observed in approximately 6500 individuals of European and African-American ancestry in the NHLB1 exome sequencing project. The R121L variant is a nonconservative amino acid substitution, which is likely to impact secondary protein structure, as these residues differ in polarity, charge, size and/or other properties. The substitution occurred at a position that is conserved across species and in silico analysis predicts this variant is probably damaging to protein structure/function. The report from this study indicates, "The pathogenic role of this missense change would be further supported if it had occurred de novo or cosegregates with the phenotype in the family." Parental testing for the CHD2 variant was recommended.

    Parental testing was done. Alas, the father has the same CHD2 variant.

  3. A 2yo girl with clinical and radiographic features suggesting Joubert syndrome is heterozygous for variants in the AHI1 (c.74A>G, p.Asp25Gly) and IFT172 genes (c.831G>C, p.Glu277Asp). A second pathogenic variant was not detected by sequencing or deletion/duplication analysis of either gene.

  4. [Revised from a comment initially posted November 26, 2016 at 7:44 pm] In a 3 yo girl with intractable epilepsy a variant of uncertain significance was detected in the GABRG2 gene and is noted c.1088G>A(p.Arg363Gln) and a variant of uncertain significance was detected in the KCNQ3 gene that is notated c.45_62del18 (p.Asp17_Gly22del). On parental testing the father has the KCNQ3 variant and the mother the GABRG2 variant.

    Pathogenic variants in GABRG2 and KCNQ3 have been seen in individuals who never develop seizures due to incomplete penetrance, so it may be possible that either of these variants is pathogenic for the patient, but is not penetrant in her parents. Penetrance is 80-85% for KCNQ3.

    It may also be possible that these variants may be confounding factors contributing to her epilepsy. There has been evidence that the presence of other variants in other ion channel proteins may influence the phenotype of GABRG2. It would be hard to prove or disprove this, but it is a possibility.

  5. A 4 1/2 yo girl with spastic paraparesis has a GBA2 variant(c.941G>A) and a PNPLA6 variant (p.Gln1193Glu) identified, genes coding for autosomal recessive disorders. A second pathogenic variant was not detected by sequencing or deletion/duplication analysis of either gene.

  6. A 3 yo boy with global developmental delay and radiographic features suggesting Joubert syndromes is heterozygous for a variant of uncertain significance in the TMEM231 gene (c.481G.A, p.Asp161Asn). No second mutation could be found.

  7. SETX follies

    A 16 months girl with ocular apraxia and a constellation of findings consistent with Joubert syndrome: Sequencing of the SETX gene was undertaken, a gene involved in ataxia with oculomotor apraxia. The patient was found to be heterozygous for a variant of unknown significance. This involved a transition C > T at nucleotide position 3809 in codon 1270 causing an amino acid change proline > leucine. I did make some inquiries after obtaining this finding. One of my correspondents, Dr. Michelle Koenig, wrote regarding the abnormality in Morgan and another two individuals of my acquaintance with SETX gene variance, “At first site, I would say that your variant looks like a private polymorphism, and there are plenty of them in this gene.” Dr. Koenig suggested that since the variants were heterozygous and silent or affecting non-conserved amino acids, these were unlikely to be relevant to her problems.

    6 year old boy with ataxia and cerebellar atrophy: SETX showed one variant of unknown significance consisting of a point mutation from G to A not corresponding to amino acid change; this was nucleotide position 6507. It was classified as a variant of unknown significance, for which the patient was heterozygous.

    17 year old adolescent male with ataxia and cerebellar atrophy: SETX showed a heterozygous T>C mutation at nucleotide position 1880. Also, there was a heterozygous KCNC3 C>G transition a nucleotide position 1344. On additional review of the genetic testing this KCNC3 mutation on chromosome 19q13.3-q13.4 which was originally reported as an unknown variant. Upon subsequent review of the literature with the help of a genetic counselor, this was reported previously as a causative mutation and is found in individuals whose classification falls under spinocerebellar ataxia 13.

  8. A 4 1/2 yo girl has genetic testing for hereditary spastic paraplegia. In GBA2 there was a variant of unknown significance c.941G>A(p.Arg314His). In PNPLA6 there was also a variant of uncertain significance c.3577C>G (p.Gln1193Glu). Both of these are autosomal recessive genes.

  9. A 3 months old female infant with brain abnormalities consistent with septo-optic dysplasia and perisylvian polymicrogyria. A comprehensive brain malformation panel performed by GeneDx revealed ADGRG1 and RELN heterozygous abnormalities.