FamilyName: Families A,B,C Founder, Pakistani

FamilyPresentingHPOs: HP:0002033,

FamilyNotHPOs:

CountryOrigin: Pakistani

Ethnicity:

Race: Asian

FamilyPreviousTesting: n/a

FamilyMethod1: same as group

FamilyMethod2: same as group

FamilyGenotypingMethod: Identified region of homozygosity on Chromosome 9, that also encoded for the genes CER1, FREM1, IFN4A, IFNA10, TEK, and IFNK. Potentially deleterious mutations were found in FREM1 and IFNA10 were noted in supplement, but when the refseq was cross referenced to gnomAD, the variants were present in a substantial number homozygotes. For a lethal conditions, this would indicate benign variation.

Affected: 7

Unaffected:

Segregations:

PublishedLOD: 4.52

eLOD: n/a

AddSegregationInfo: All families from Pakistani origin. Family A and C were Pakistani. Family B was from Kashmir, on the Pakistani border.

ProbandLabel: Family A-IV:6/ CaseA IV:6, male, Pakistani, died as 12 days old

Homozygous

Variant: NM_001031689.2(PLAA):c.68G>T (p.Gly23Val)

ClinVar or CAID: 427941

gnomAD: n/a

FamilyAddInfo:

FamilyPMIDs:

CasePresentingHPOs: HP:0025116, HP:0001561, HP:0008872, HP:0008936, HP:0002509, HP:0002033, HP:0002015, HP:0001007, HP:0003196, HP:0000343, HP:0000218, HP:0000369, HP:0007598, HP:0100259, HP:0010576, HP:0007633, HP:0031605, HP:0000851, HP:0011968, HP:0100022, HP:0002871, HP:0001522

CaseNOTHPOs:HP:0001507

AddCaseInfo:

VariantEvidence: PLAA G23V homozygous mice were generated by Crispr/Cas9 genome editing. Examination of PLAA protein levels in the cerebellum of the homozygous G23V mutant mice vs the wildtype littermates (Figure 3A) revealed significantly reduced protein expression, indicating the G23V variation effects protein stability, and indicates a loss of function mechanism for the variant.

Score: Default for homozygous missense.

Note: Will score the phenotypes associated with the G23V mouse as experimental evidence seperately.

Case: Family D-Case VIII-1, male, Saudi Arabia, died at 10 months

CasePresentingHPOs: HP:0005957, HP:0030917, HP:0005972, HP:0000414, HP:0000400, HP:0000343, HP:0100259, HP:0002069, HP:0001649, HP:0002104, HP:0011294, HP:0007204, HP:0002536, HP:0002719

CasePresentingHPOText: Authors note his birth weight was 2.3 kg, length 55cm and OFC 30.2cm. Noted as having frequent negative Rolandic sharp waves and fronto-central sharp waves on EEG on the 2nd day of life. Seizures manifestation occured with hyper-rhythmic discharges that emanated from the right frontal and centro-occipital regions. Intractable seizures on keppra, added oral pyridoxine at 2 months with improvement of seizure control. Proband had reccurrent chest infections and died at 10 months of life.

CaseNOTHPOs:

CasePreviousTesting: n/a

CaseGenotypingMethod: Homozygosity mapping and exome sequencing.

Homozygous, parental testing confirmed in trans.

Variant: NM_001031689.2(PLAA):c.68dup (p.Leu24Profs)

ClinVar ID: 427942

Pathogenic, no star, last reviewed Jun 21, 2017. Duplication/ frameshift

gnomAD: n/a

AddCaseInfo: Figure of Pedigree in Fig S1 Family D. Only the proband is homozygous, all others tested were shown to be heterozygous carriers (indicated by the center dots). The father had two brothers that were noted to have the same phenotype that resulted in lethality, but they were not able to be genotyped.

VariantEvidence: n/a

ExperimentName: Plaa G23V/G23V homozygous mice

NonHumanModel: mus musculus

GeneAlteration: Crispr/Cas9 gene editing was used to successfully mutate the mouse Plaa gene with a patient derived variant, G23V (mouse c. 68G>T) (Figure 3 and Figure S4). From the first round of injections, the obtained 33 mice, in which 3 had the c.68G>T variation alone/ solely. Confirmation of the change was performed by Sanger sequencing in the founder mice.

ModelPhenotype: HP:0004325, HP:0002808, HP:0001337, HP:0012448

HumanPhenotype: HP:0012448

ModelEvidence: Plaa G23V homozygous mice are viable past birth, but cannot survive past 6 months without assistance of feeding, etc (Figure 3B). The mutant show microcephaly (reduced brain volume, Figure 3C). MRI performed on the G23V homozygous mice compared with control wildtype littermates show significantly reduced corpus callosum and cerebellum volumes, indicating reduced white matter (Figure 3E). The cerebellum is noted to have disrupted foliation (figure S5C). The authors note early onset neurodysfunction, including tremor and muscle weakness , showing severe hindlimb clasping, reduced grip strength and altered gait detectable from P14 (Figure 3 and Figure S5).

They authors even went on to cross the Plaa G23V heterozygous mice with Plaa homozygous null mice to create Plaa G23V/- mice that have a more severe phenotype that the homozygous Plaa G23V homozygous, but less severe that the Plaa homozygous null (plaa-/-).

EvidenceShown: Figure 3, Figure S3-6,

ModelVariant: NM_001031689.2(PLAA):c.68G>T (p.Gly23Val)

ClinVar ID: 427941

Score:

Reason: This mouse model represents a patient derived mutation that was knocked directly into the mouse Plaa locus, through use of Crispr/Cas9 gene editing. The mice were shown to have reduced Plaa protein expression (reduced by 70%), and the development of phenotypes consistent with phenotypes observed in individuals. I have therefore, increased the score based on the evidence provided.

Score: 3

FamilyName: PLAA L752F Founder families

FamilyPresentingHPOs: HP:0002061, HP:0002191, HP:0006986, HP:0002273, HP:0002493, HP:0001332, HP:0001332, HP:0011344, HP:0031826, HP:0002267

FamilyHPOFreeText: Posture deformation, including dystonic posturing, rigidity and freezing.Motor delay was severely impaired and classified as Level V according to the Gross Motor Function Classification System.

FamilyNotHPOs:

CountryOrigin: Israel

Ethnicity:

Race:

FamilyPreviousTesting:

FamilyMethod1: Linkage and haplotype analysis

FamilyMethod2: mIPs-Gene panels

FamilyGenotypingMethod: Linkage and haplotype analysis revealed a common founder mutation between Families 1/A and 2/B (Figure 2). mIP technology was used for gene sequencing to confirm the genetic alteration of the PLAA gene, in homozygosity. Confirmation of the PLAA variant was done by Sanger Sequencing.

Affected: 7

Unaffected: 23

Segregations:

PublishedLOD: 3.24

eLOD: n/a

AddSegregationInfo: Families 1/A and 2/B were found to share a common ancestor, and thus revealed a founder mutation.

ProbandLabel: Family A-VI3, female, AoO= 4 months, AaR= 15 years

Variant: NM_001031689.2(PLAA):c.2254C>T (p.Leu752Phe)

ClinVar: 427940

Hoomzygous, Asserted Pathogenic on ClinVar, no star, updated June 21, 2017

gnomAD: n/a

FamilyAddInfo:

FamilyPMIDs: n/a

CasePresentingHPOs: HP:0001508, HP:0000253, HP:0003487, HP:0007103, HP:0012448, HP:0012444, HP:0002808, HP:0000768, HP:0000998, HP:0005692, HP:0001371, HP:0001838, HP:0007410, HP:0012713, HP:0007377, HP:0009051

CasePresentingHPOsFreeText: The delayed myelination was noted along corticospinal tract and posterior genu of capsula interna at age 13 months of age. Brain atrophy noted at 3.5 years old. Central bilateral disturbance in central tract conduction above the brainstem noted by somatosensory evoked potentials (SSEP). Sedimentation of glycogen like material (PAS positive) in muscle biopsy.

CaseNOTHPOs: HP:0001250

CaseNOTHPOSFreeTExt: Normal respiratory chain.

VariantEvidence: Molecular modeling revealed the the Leu752Phe variant is likely to disrupt the PUL domain and may result in an alteration of the protein structure that could affect function (Fig. 2E). Examination in patient derived cells shows that the Leu752Phe variant disrupts the ability of PLAA to induce prostoglandin biogenesis (Fig. 4). As this mechanism is not known to be disease related, it does show an alteration of the protein function by the variant, thus supporting pathogenicity.