MonDO: MONDO:0032706

Case: Patient NIJ. 46 year old Dutch/Egyptian female onset of gait difficulties at age 34 with progressive worsening. Analysis of the maternal DNA revealed that she carries the p.Gln316* mutation, but not the frameshift mutation, indicating that the mutations in the proband are on opposite alleles.

DiseaseAssertion: Cerebellar ataxia

FamilyInfo:

CasePresentingHPOs: HP:0001288, HP:0007979, HP:0008003, HP:0007338, HP:0001251, HP:0002064, HP:0006895, HP:0001348 (Gait disturbance, Gaze-evoked horizontal nystagmus, Jerky ocular pursuit movements, Hypermetric saccades, Ataxia, Spastic gait, Lower limb hypertonia, Brisk reflexes

CaseHPOFreeText: Difficulty writing, cerebellar dysarthria, downgoing plantar responses, ataxia on finger chase and heel-shin slide, Mild spastic paraplegia Cervical dystonia

CasePreviousTesting: No weakness. Normal sensory examination. An MRI brain scan revealed mild cerebellar atrophy. Ophthalmological examinations were normal. Nerve conduction studies and EMG did not show evidence of a peripheral neuropathy. Laboratory testing including vitamin E, metabolic screening, albumin, cholesterol, alpha-fetoprotein, lactate, acanthocytes, copper, ceruloplasmin, and coeliac screen was normal or negative. Genetic testing for Friedreich, spinocerebellar ataxias (SCAs) 1, 2, 3, 6, 12, 14 and 17, dentatorubral-pallidoluysian atrophy, autosomal recessive spastic ataxia of Charlevoix-Saguenay and SPG7 were negative.

GenotypingMethod: Exome sequencing. Sanger sequencing was performed for confirmation of the variants and for segregation analyses using standard techniques. Altogether, 117 708 variants (single nucleotide variants and small deletions/insertions/indels) were detected. Initial filtering for a gene panel of movement disorders revealed no mutations.Variants were filtered for variant type, rarirty (MAF <0.5%) and conservation (>0.75, phyloP). Paternal DNA unavailable.

MultipleGeneVariants:

(1) GeneName: GDAP2

(1) Variant: c.946C>T; p.(Gln316*)

(1) ClinVarID or CAID: CA1031513

(1) gnomAD: Total AF 0.00006711 (gnomAD v4.1, https://gnomad.broadinstitute.org/variant/1-117896840-G-A?dataset=gnomad_r4)

(2) GeneName: GDAP2

(2) Variant: c.1305dup p.(Ser436fs*36)

(2) ClinVarID or CAID: CA913189981

(2) gnomAD: Total AF 0.000001301, gnomAD v4.1 (https://gnomad.broadinstitute.org/variant/1-117878149-A-AC?dataset=gnomad_r4)

MonDO: MONDO:0032706

Case: Patient AW, Belgian female developed mild gait imbalance at age 38 years with progressive decline with clear dementia at age 53 years. She died at age 62 years due to infectious complications. Homozygous for GCAP2:c.1198_1199insG; p.(His400fs*15). The variant and its segregation were confirmed in the proband and her daughter using standard Sanger sequencing methodology.

DiseaseAssertion: Cerebellar ataxia

FamilyInfo: No consanguineous family. Her brother died from brain tumor, her father had epilepsy and died at 84 years old, her mother was alive without ataxia or gait disorder at age 85 years. Daughter is healthy.

CasePresentingHPOs: HP:0002141, HP:0007240, HP:0001348, HP:0033687, HP:0000708, HP:0002061, HP:0002540, HP:0001268, HP:0000741, HP:0000718, HP:0000716, HP:0002546, HP:0002015, HP:0002300, HP:0000726 (Gait imbalance, Progressive gait ataxia, Brisk reflexes, Short term memory impairment, Atypical behavior, Lower limb spasticity, Inability to walk, Mental deterioration, Apathy, Aggressive behavior, Depression, Incomprehensible speech, Dysphagia, Mutism, Dementia

CaseHPOFreeText: Speech problems, jerky eye movements, dysexecutive syndrome, bed ridden

CaseNOTHPOs: HP:0000639 (Nystagmus)

CasePreviousTesting: Brain MRI at age 53 years revealed severe atrophy of the cerebellum, both vermian and hemispheric, mainly of the superior aspect, and also global cerebral atrophy (cortical and central). Levels of alpha-fetoprotein, vitamin E, copper, and folic acid were normal. Screening for trinucleotide repeat expansions was negative for SCAs 1, 2, 3, 6, 7, 8, 10, 12, and 17, and for Friedreich’s ataxia. Post-mortem brain examination revealed cerebellar atrophy in combination with a mild atrophy of the pes pontis. Normal nerve conduction studies. Normal opthalmological evaluation.

GenotypingMethod: Exome sequencing. Sanger sequencing was performed for confirmation of the variants and for segregation analyses using standard techniques. 90 560 single-nucleotide variations and 8961 indels were called. No obvious variants in known ataxia genes were observed. Variants were filtered for variant type, rarirty (MAF <0.5%) and conservation (>0.75, phyloP). Trio-sequencing analysis to detect putativede novo variants was not possible because of the unavailability of paternal DNA for Patient NIJ and parental DNA for Patient AW.

Variant: c.1198_1199insG; p.(His400fs*15) Homozygous

ClinVarID: 624620

CAID: CA30125084

gnomAD: Total AF 0.000004342, gnomAD v4.1. https://gnomad.broadinstitute.org/variant/1-117883536-T-TC?dataset=gnomad_r4

Functional evidence: Drosophila fly GDAP2 model supports a role of GDAP2 in motor behaviour and suggests that cellular stress might be driving the neurodegenerative cascade. Ubiquitous Gdap2 RNAi-1 knockdown results in droopy wings. Gdap2 knockdown does not result in increased levels of apoptotic cell death in central brain upon 18 hours paraquat exposure.

MonDO: MONDO:0032706

Case: 58-year-old male of Greek origin presenting with a progressive cerebellar syndrome starting at the age of 33 years with mild gait imbalance, ataxia and dysarthria. Apart from dyslipidaemia, type 2 diabetes, and chronic diarrhoea presenting at 37 years of age and attributed to irritable bowel syndrome, the rest of the patient’s medical history is unremarkable. Proband has NM_017686.4; c.134delC with mother as carrier.

DiseaseAssertion: Cerebellar ataxia

FamilyInfo: His relatives have reported personality changes with emotional lability, aggressive behaviour and depressive episodes. Family history is negative for neurological disorders. Both parents originated from the same small village but there was no known consanguinity in the family

CasePresentingHPOs: HP:0002141, HP:0002070, HP:0002066, HP:0001260, HP:0003119, HP:0005978, HP:0002028, HP:0000726 (Gait imbalance, Limb Ataxia, Gait Ataxia, Dysarthria, Abnormal circulating lipid concentration, Type II diabetes mellitus, Chronic diarrhea, Dementia)

CasePreviousTesting: Neurological examination at the age of 50, when the proband was first seen, showed severe gait ataxia with mild pyramidal features consisting of brisk reflexes, dysmetria, dysdiadochokinesia, cerebellar dysarthria, jerky pursuit and nystagmus, mild behavioural changes, and disturbances of short-term memory. Follow-up neurological examination at the age of 58, revealed severe gait disturbance, dysmetria, dysdiadochokinesia and brisk deep tendon reflexes with flexor plantar responses, as well as gaze-evoked nystagmus, jerky pursuit, hypermetric saccades, cerebellar dysarthria, and mild sensory loss in the lower limbs (Supplementary Video 1). Scale for the assessment and rating of ataxia (SARA) score at that time was 31/40 and Mini-Mental State Examination (MMSE) score was 24/30. A detailed neuropsychological assessment was performed, revealing widespread deficits in encoding, learning, and consolidating new verbal information. Overall, the patient exhibited prominent deficits in episodic memory, verbal working memory, and executive functions. A brain MRI scan, including susceptibility-weighted imaging (SWI), was performed and revealed marked cerebellar atrophy affecting the hemispheres and more significantly the vermis, as well as mild cortical atrophy, midbrain and pons atrophy. Nerve conduction studies (NCS), electromyography (EMG) and ophthalmological evaluation were all normal. Laboratory testing of alpha-fetoprotein levels, vitamin E, copper, and folic acid were also normal. To exclude the possibility of an underlying autoimmune disease, the patient’s serum was tested for binding to various markers, including a panel of paraneoplastic markers of autoimmunity, GAD, NMDA, AMPA, GABAB, DPPX and VGKC, as well as monkey cerebellum frozen tissue. No binding to any of these markers was detected.

GenotypingMethod: Blood samples from the proband and his mother were collected for whole exome sequencing ans Sanger confirmation. Initial screening for Friedreich’s ataxia, as well as spinocerebellar ataxia (SCA) types 1, 2, 3, 6 and 7 in the proband was negative.

Variant: GDAP2:c.134del, p.(Pro45Leufs*22)

CAID: CA2574039871

gnomAD: Total AF 0.000001866, gnomAD v4.1 (https://gnomad.broadinstitute.org/variant/1-117920223-AG-A?dataset=gnomad_r4)

MonDO: MONDO:0032706

Case: Chinese male. Onset at age 30 years with mild dysarthria with progressive worsening.

DiseaseAssertion: Cerebellar ataxia

FamilyInfo: No history of neurological disease and consanguinity was documented in the family. Delivery and perinatal events were unremarkable.

CasePresentingHPOs: HP:0001260, HP:0002141, HP:0002061, HP:0009046 (Dysarthria, Gait imbalance, Lower limb spasticity, Difficulty running

CaseHPOFreeText: Difficulty writing, Increase in bilateral knee reflexes

CaseNOTHPOs: HP:0003487 (Babinski sign)

CasePreviousTesting: His clinical examination displayed cerebellar ataxia with abnormal finger-to-nose and heel-knee-shin tests. Bilateral knee reflexes were symmetrical increased (+++) and Babinski signs were negative. Cranial nerves, muscle strength and sensory examinations were normal. Mild cognitive decline with a Mini-Mental State Examination (MMSE) of 24/30, a Scale for the Assessment and Rating of Ataxia (SARA) score of 17.5/40 and International Cooperative Ataxia Rating Scale (ICARS) score of 46/100. Brain MRI revealed cerebellar atrophy (Fig. 1A).

GenotypingMethod: WES with Sanger confirmation and co-segregation analysis. Genetic testing for spinocerebellar ataxias (SCAs) 1, 2, 3, 6, 7, 12, 17 and dentatorubral-pallidoluysian atrophy (DRPLA) were negative.

VariantEvidence: Wildtype and mutant plasmids were transfected into SH-SY5Y cells. The mRNA level of frameshift variant p.Thr442fs7 was almost same with the level of wild-type, whereas nonsense variant p.Arg253 was even increased, thus they might escape NMD. As a result, p.Gln316 and p.Ser436fs36 mutant GDAP2 proteins were barely detectable, p.Thr442fs7, p.His400fs15 and p.Arg253 generated truncated proteins. Western blot analysis indicated that the GDAP2-Arg253 and GDAP2-Thr442fs*7 were C-terminal deletion mutants.

MultipleGeneVariants:

(1) GeneName: GDAP2

(1) Variant: c.757C>T (p.Arg253*)

(1) ClinVarID or CAID: CA1031554

(1) gnomAD: Total AF 0.00001860, gnomAD v4.1 (https://gnomad.broadinstitute.org/variant/1-117899096-G-A?dataset=gnomad_r4)

(2) GeneName: GDAP2

(2) Variant: c.1323delC (p.Thr442fs*7)

(2) ClinVarID or CAID: CA2586967196

(2) gnomAD: not found in gnomAD v4.1