FamilyPY: White, United Kingdom

FamilyPresentingHPOs: HP:0002131, HP:0001260, HP:0008003, HP:0030453 (Episodic ataxia, Dysarthria, Jerky ocular pursuit movements, Abnormal visual electrophysiology)

HPOsFreeText: N/A

FamilyNotHPOs: HP:0000640, HP:0000648, HP:0003390, HP:0011402, HP:0001272, HP:0002283 (Gaze-evoked nystagmus, Optic atrophy, Sensory axonal neuropathy, Demyelinating sensory neuropathy, Cerebellar atrophy, Global brain atrophy)

NotHPOsFreeText: N/A

FamilyGenotypingMethod: Blood genomic DNA was enriched and whole exome sequenced. Alightment to hg19 and variant filtering was performed with putative pathogenic variants being confirmed via Sanger sequencing.

FamilyPreviousTesting: Underwent brain MRI and CSF examination with oligoclonal band analysis; Negative genetic testing for SCA1, 2, 3, 6, 7, 17 (now known as ATXN1, ATXN2, CACNA1A, ATXN7, and TBP, respectively), DRPLA (now known as ATN1), FA (now known as FXN) and FMR1

FamilyAddInfo: N/A

Variant: NM_004172.5(SLC1A3):c.1496G>A (p.Arg499Gln)

ClinVar: 242994, https://www.ncbi.nlm.nih.gov/clinvar/variation/242994/

gnomAD: 0.0001471, https://gnomad.broadinstitute.org/variant/5-36686238-G-A

Affected: 3

Segregations: 2

AddSegregationInfo: Pedigree in Sup Data, Not enough info provided

NonHumanModel: Mouse (Mus musculus)

GeneAlteration: A fragment covering exons 4-8 of the SLC1A3 locus was subcloned with the P290R seuqnece being inserted via PCR into the end of Exon 7. Thse clones were injected into blastocysts of C37BL/6N mice with these generatingfoster mice and chimeric mice being crossbred to excise the neomycin casette. Due to the high mortality rate, the surviving mice harboring the variant were backcrossed to 129/SvJ for a more robust mouse and higher survival rate for study.

ModelPhenotype: MP:0002064, MP:0001393, MP:0010387, MP:0008925, MP:0002182, MP:0000877, MP:0010170, MP:0014185 (Seizures, Ataxia, Abnormal Bergmann glial cell morphology, Increased cerebellar granule cell number, Abnormal astrocyte morphology, Abnormal Purkinje cell morphology, Abnormal glial cell apoptosis, Cerebellum atrophy)

ModelFreeText: Slower firing of purkinje neurons

HumanPhenotype: HP:0001251, HP:0002076, HP:0001250 (Ataxia, Migraine, Seizure)

HumanFreeText: N/A

ModelEvidence: The first set of mutant knock-in mice were subject to generalized seizures and death before the weaning period, requiring a backcross onto the 129/SvJ strain in order to reduce lethal seizure activity and delay the onset. Even so, mutant mice demonstrated significant phenotypes indicative of human Episodic Ataxia including epilepsy, ataxia, and reduced motor/gait coordination. In order to determine the pathogenc mechanism, cerebellar Bergmann glia cells were examined to find a pronounced age-dependent reduction of cell numbers between P10 and P20. Immunostaining showed decreased numbers of somata and expression, demonstrating that the EAAT1 mutants were subject to cell death. Granule cell migration was also impaired during development, coupled with invasion of reactive astrocytes into the molecular layer demonstrating attempted repair. Following from this change, Purkinje neurons were examined and found to have been reduced and the morphology altered in mutant mice. As the P290R variant is known to increase EAAT1 anion currents in heterologous expression systems, measurement of these currents in mouse Bergmann glia cells showed significantly increased current, decreased Cl- concentration, and a resulting higher TUNEL expression in these cells, indicating earlier apoptosis events of these cell types. Spiking activities and developmental acceleration is absent in these cell types, likely due to progressive deterioration. This was verified by an observation of cerebellar size, where mutant cerebellar tissue showed generalized degeneration compared to the WT mice.

ModelVariant: NM_004172.5(SLC1A3):c.869C>G (p.Pro290Arg)

ClinVar: 9441, https://www.ncbi.nlm.nih.gov/clinvar/variation/9441/

CaseKO: Male, 22 yrs report, Serbia

CasePresentingHPOs: HP:0002076, HP:0002017, HP:0000505, HP:0002357, HP:0003474, HP:0004302, HP:0001269, HP:0012229, HP:0011288, HP:0002321, HP:0000622 (Migraine, Nausea and vomiting, Visual impairment, Dysphasia, Sensory impairment, Functional motor deficit, Hemiparesis, CSF pleocytosis, EEG with parietal sharp slow waves, Vertigo, Blurred vision)

HPOsFreeText: Mechanosensitivity

CaseNotHPOs: HP:0011182, HP:0001251, HP:0001250 (Interictal epileptiform activity, Ataxia, Seizure)

NotHPOsFreeText: N/A

CaseAddInfo: No evidence of headache attacks with focal neurological deficits in any other family member, but the patient’s father was found to suffer from migraine without aura

CasePreviousTesting: Responsive to treatment with ibuprofen; Mild head trauma is a trigger; Neuroimaging during attacks was normal; Screen for variants in CACNA1A, ATP1A2, SCN1A, and PRRT2 was negative

CaseGenotypingMethod: All exons and exon-intron boundaries of the SLC1A3 gene were seuqenced and a variant was found that segregates with the phenotype.

Variant: NM_004172.5:c.1159A>C (p.Thr387Pro)

CAID: CA359482299, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA359482299

gnomAD: Not in gnomAD

CaseJE: Male, 10 yrs report,

CasePresentingHPOs: HP:0002131, HP:0004374, HP:0001319, HP:0001270, HP:0001350, HP:0002076, HP:0010547, HP:0001272, HP:0002381, HP:0002181, HP:0011182, HP:0045084, HP:0001289, HP:0002078, HP:0007034, HP:0007772, HP:0011289 (Episodic ataxia, Hemiplegia/hemiparesis, Neonatal hypotonia, Motor delay, Slurred speech, Migraine, Muscle flaccidity, Cerebellar atrophy, Aphasia, Cerebral edema, Interictal epileptiform activity, Limb myoclonus, Confusion, Truncal ataxia, Generalized hyperreflexia, Impaired smooth pursuit, EEG with temporal sharp slow waves)

HPOsFreeText: Left visual field neglect, Episodic left hemifield distortion

CaseNotHPOs: HP:0000639, HP:0000570, HP:0007670, HP:0000267 (Nystagmus, Impaired saccades, Abnormal vestibulo-ocular reflex, Cranial asymmetry)

NotHPOsFreeText: N/A

CaseAddInfo: Variant is confirmed heterozygous de novo via parental testing and confirmed paternity; No family member has any neurological signs or symptoms

CasePreviousTesting: Previously screened for CACNA1A and ATP1A2 with negative results; Episodic migraine attacks led to progressive right-sided headache and left-sided symptoms such as weakness and visual field neglect; Comprehensive metabolic workup revealed no abnormality in the CSF, serum, and urine; MRI showed a diffuse right-sided cortical hyperintensity most prominent in fluid-attenuated inversion recovery (FLAIR); EEG showed subclinical seizure activity in the left frontal temporal cortex and diffuse slowing on the right

CaseGenotypingMethod: DNA was extracted from blood samples. All exons and flanking intronic regions of SLC1A3 were PCR-amplified and directly sequenced. These were confirmed via resequencing.

Variant: NM_004172.5(SLC1A3):c.869C>G (p.Pro290Arg)

ClinVar: 9441, https://www.ncbi.nlm.nih.gov/clinvar/variation/9441/

gnomAD: Not in gnomAD

CaseKDC23: Male, 38 yrs onset, Korea, Asian

CasePresentingHPOs: HP:0002131, HP:0002321, HP:0001260, HP:0000640, HP:0011477, HP:0100543 (Episodic ataxia, Vertigo, Dysarthria, Gaze-evoked nystagmus, Upbeat nystagmus, Cognitive impairment)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Proband has no family history of disease

CasePreviousTesting: Negtive response to acetazolamide

CaseGenotypingMethod: Next-generation sequencing was perfomed on all probands with 40 candidate genes and five known EA genes.

Variant: NM_004172.5:c.952A>G (p.Thr318Ala)

CAID: CA3235581, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA3235581

gnomAD: 0.002656, https://gnomad.broadinstitute.org/variant/5-36679820-A-G NOTE EXTREMELY HIGH gnomAD FREQUENCY

FamilyKDC: Korea

FamilyPresentingHPOs: HP:0001251, HP:0002321, HP:0002018 (Ataxia, Vertigo, Nausea)

HPOsFreeText: N/A

FamilyNotHPOs: N/A

NotHPOsFreeText: N/A

FamilyGenotypingMethod: Genomic DNA was extracted fom patient blood samples. Whole exome sequencing was performed. Sequence variants in KCNA1, CACNA1A, CACNB4 and SLC1A3 were all searched with pathogenicity-based variant filtering. The found variant was further confirmed via PCR and Sanger sequencing.

FamilyPreviousTesting: Ataxic episodes usually provoked by stress; Responded to treatment with acetazolamide

FamilyAddInfo: N/A

Variant: NM_004172.5:c.1177G>A (p.Val393Ile)

CAID: CA3235626, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA3235626

gnomAD: 0.0002940, https://gnomad.broadinstitute.org/variant/5-36680579-G-A NOTE FREQUENCY VERY HIGH

Affected: 2

Segregations: 1

AddSegregationInfo: NOTE INCONSISTENT SEGREGATIONS, Not enough info to count, Pedigree in Figure 1A

FamilyDEVR: Europe

FamilyPresentingHPOs: HP:0002078, HP:0002066, HP:0002321, HP:0002017, HP:0000613, HP:0002183, HP:0000639 (Truncal ataxia, Gait ataxia, Vertigo, Nausea and vomiting, Photophobia, Phonophobia, Nystagmus)

HPOsFreeText: N/A

FamilyNotHPOs: HP:0002411 (Myokymia)

NotHPOsFreeText: N/A

FamilyGenotypingMethod: Genomic DNA was isolated from peripheral leukocytes. All exons and flanking introns of the SLC1A3 gene were amplified and sequenced. Restriction digest verified the results.

FamilyPreviousTesting: Attacks were generally triggered by emotional stress, with some triggered by fatigue; Acetazolamide significantly reduced the frequency of attacks in all 3 affected family members;

FamilyAddInfo: N/A

Variant: NM_004172.5(SLC1A3):c.556T>A (p.Cys186Ser)

ClinVar: 9442, https://www.ncbi.nlm.nih.gov/clinvar/variation/9442/

gnomAD: Not in gnomAD

Affected: 4

Segregations: 2

AddSegregationInfo: Not enough info

CasePAII-1: Female, 18 yrs onset

CasePresentingHPOs: HP:0000147, HP:0040292, HP:0002083, HP:0003401, HP:0001251, HP:0000640, HP:0006855, HP:0006744 (Polycystic ovary disease, Left hemiplegia, Migraine without aura, Paresthesia, Ataxia, Gaze-evoked nystagmus, Cerebellar vermis atrophy, Adrenocortical carcinoma)

HPOsFreeText: N/A

CaseNotHPOs: HP:0000505 (Visual impairments)

NotHPOsFreeText: N/A

CaseAddInfo: Parents are consanguineous, Mother has similar symptoms but declined to be clinically examined

CasePreviousTesting: Episodes triggered by menstruation but also by stress and preceded by a sensorimotor march; EEG and electroneurography were normal; Pathologic CAG expansions in CACNA1A and conventional mutations in CACNA1A, ATP1A2, and SCN1A were ruled out; Treatment with ACZ (250 mg twice daily) prevented hemiplegic spells and interictal GEN receded; MRS demonstrated low combined glutamate and glutamine peak that responded to ACZ treatment during an episode

CaseGenotypingMethod: Targeted genotyping analysis was performed.

Variant: NM_004172.5:c.379_383del (p.Tyr127Aspfs*60)

CAID: CA1139532263, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA1139532263

gnomAD: Not in gnomAD

CaseIW: Female, 10 yrs report,

CasePresentingHPOs: HP:0002078, HP:0000486, HP:0002080, HP:0001350 (Truncal ataxia, Strabismus, Intention tremor, Slurred speech)

HPOsFreeText: Hypoperfusion of cerebellum and brainstem at 8 yrs

CaseNotHPOs: HP:0001270 (Motor delay)

NotHPOsFreeText: N/A

CaseAddInfo: Parents are healthy and non-consanguineous and have no family history of neurological symptoms; Proband is confirmed de novo heterozygous via parental testing

CasePreviousTesting: Treatment with acetazolamide helped with symptoms

CaseGenotypingMethod: Genomic DNA was isolated from peripheral blood leukocytes and subject to whole exome sequencing. Variants were filtered according to likely pathogenicity and presence in previously reported causative genes associated with ataxia, cerebellar atrophy, and other neurodegenerative diseases.The SLC1A3 variant was confirmed via Sanger seuqencing in the proband and absent in her parents.

Variant: NM_004172.5:c.383T>G (p.Met128Arg)

CAID: CA359477326, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA359477326

gnomAD: Not in gnomAD