Case: Individual 13, male, AOR= 8 years 4 months

CasePresentingHPOs: HP:0000252, HP:0000750, HP:0001263, HP:0001290, HP:0000527, HP:0006332, HP:0001212, HP:0004279, HP:0000202, HP:0010289, HP:0000540

CasePresentingHPOText: Began walking 18 Noted as limited vocabulary and saccadic speech. Noted to have short fingers.

CaseNOTHPOs: HP:0001250, HP:0002376, HP:0002360, HP:0000708, HP:0000924, HP:0002719

CaseNOTtextHPO: no ID per the WISC-V. CT scan normal

CasePreviousTesting: Karyotyping, Fragile X Syndrome (FMR1), and Array-CGH (Agilent 180K) were all normal

CaseGenotypingMethod: Trio WES (exome capture Agilent CRE and HiSeq 4000).

Variant: hg19:chr2: g.4804618 6_4804619 0del, c.1825_1829del, p.(Glu609) OR* NM_001190274.1:c.1825_1829del

CA ID: CA658820930

de novo

gnomAD: n/a

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VariantEvidence: The Gln609Ter mutation occurs in exon 15 which encodes the second CASH domain. The nonsense mutation most likely disrupts the second and third CASH domains and the zinc-finger ubiquitin binding region. No functional assays or variant evidence was provided, so I have downgraded the score.

Case: Individual 15, male, AOR= 11 years 5 months

CasePresentingHPOs: HP:0002167, HP:0002342, HP:0001250, HP:0002376, HP:0002360, HP:0000717, HP:0007018, HP:0000718, HP:0000735, HP:0002553, HP:0000154, HP:0000289, HP:0000179, HP:0000293, HP:0009909, HP:0004209, HP:0000403, HP:0009921, HP:0002020

CasePresentingHPOText: Began walking at 14 months old. Noted as having limited vocabulary, short sentences and single words. Noted as having one single seizure at 5 years old. Developmental regression noted at 1 year old. Has food seeking behavior.

CaseNOTHPOs: HP:0000202, HP:0000924,

CaseNOTtextHPO:

CasePreviousTesting: ArrayCGH, Prader will and Anglican syndrome methylation studies, and RAI1 analysis (by DHPLC) were all normal

CaseGenotypingMethod: Trio-WES performed through the DDD consortium, 2017 PMID:PMID: 28135719.

Variant: hg19:chr2: g.4804051 5_4804052 2dup, c.2084- 6_2085dup, p.(Gly697) OR* NM_001190274.1:c.2084-6_2085dup

CA ID: CA658765223

de novo

gnomAD: n/a

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VariantEvidence: The c.2084−6_2085dup id suggested to lead to a stop codon at Gly697, which is located in exon 18. Exon 18 is upstream of the third CASH domain, which regulates substrate recognition. No functional assays or variant evidence was provided, so I have downgraded the score.

Case: Individual 3, male, 7.5 yo

CasePresentingHPOs: HP:0000750, HP:0001263, HP:0001290, HP:0002360, HP:0007018, HP:0000736, HP:0004673, HP:0000735, HP:0000629, HP:0000316, HP:0004209, HP:0001212, HP:0001382,

CasePResentingHPOText: Subject began walking at 18 months. Testing for autism gave the following results: WPPSI-III-NL: TIQ 98, VIQ 106, PIQ 96.

CaseNOTHPOs: HP:0001250, HP:0002376, HP:0000202, HP:0000504,

CasePreviousTesting: Metabolic screening, SNP-array, and Fragile X (FMR1) testing were normal

CaseGenotypingMethod: Trio-WES. Individual is noted as being mosaic (60%) for the FBXO11 mutation. Testing also identified a VUS in TP73 (NM_0054 27.3):chr1: g.3644250 G>A, c.901G>A; p.(Asp301Asn). Not noted as de novo, so assume inherited and parents were not noted as having behavioral abnormalities or intellectual disability.

Variant: hg19:chr2: g.4806611 8=/T>C, c.467=/A> G p.(Gln156Arg) or NM_001190274.1:c.467A>G

CA ID: CA346813225

de novo Trio-WES performed so maternity and paternity could be investigated with this method.

gnomAD: n/a

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VariantEvidence: Individual is noted as being mosaic (60%) for the FBXO11 mutation. Gln156 is located just N-terminal to the F-box region of FBXO11, and is conserved across species. Pathogenicity algorithms showing varying predictions, from tolerated to damaging, thus indicating a VUS. No functional assays were performed to indicate the impact of the Q156R mutation on FBXO11 function.

Case: Individual 9, male, AOR= 3 years 10 months

CasePresentingHPOs:  HP:0004322, HP:0004325, HP:0000252, HP:0001263, HP:0001611, HP:0001256, HP:0001290, HP:0002360, HP:0000736, HP:0030213, HP:0001090, HP:0002553, HP:0000527, HP:0000494, HP:0000316, HP:0000426, HP:0000455, HP:0000322, HP:0000219, HP:0000307, HP:0000179, HP:0000400, HP:0011271, HP:0200055, HP:0009836, HP:0001212, HP:0001852, HP:0000565, HP:0000915

CasePresentingHPOText: Began walking at 13 months, first words at 23 months. Intelligence testing should an IQ of 75-88 but noted as uneven profile.

CaseNOTHPOs: HP:0001250, HP:0002376, HP:0000202

CasePreviousTesting: Affymetrix Cytoscan Array screening was normal

CaseGenotypingMethod: Individual WES (Illumina HiSeq 2500), filtering against known and candidate genes from SysID (by Konchinke et al., 2016 PMID: 26748517). Sanger sequencing for confirmation and to test the parents and show absence of the variant. The sample identity was also confirmed.

Variant: hg19:chr2: g.4806682 1_4806682 2del, c.319_320 del, p.(Leu107Alafs45) OR* NM_001190274.1:c.319_320del

CA ID: CA658820927

de novo

gnomAD: n/a

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VariantEvidence: The Leu107Alafs*45 mutation causes a frameshift mutation and premature stop codon. The mutation start in exon 2 and thus removes the F-BOX, all three CASH domains and the zinc-finger UBR region, thus it should act as a loss of function variation. No functional assays or variant evidence was provided.

Case: Individual 10, female, AOR= 5 years

CasePresentingHPOs: HP:0000252, HP:0001256, HP:0008935, HP:0002360, HP:0000736, HP:0012434, HP:0000712, HP:0012171, HP:0000490, HP:0030820, HP:0000431, HP:0004467, HP:0000218, HP:0010296, HP:0001010

CasePresentingHPOText: Began walking at 15 months, no notation on speech.

CaseNOTHPOs: HP:0001250, HP:0002719, HP:0000924, HP:0000202, HP:0001155, HP:0001760, HP:0000478, HP:0002719

CasePreviousTesting: No previous testing

CaseGenotypingMethod: Trio-WES.

Variant: hg19:chr2: g.4806607 8_4806607 9del, c.506_507del, p.(Ser169Leufs9) OR* NM_001190274.1:c.506_507del

CA ID: CA658820928

de novo

gnomAD: n/a

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VariantEvidence: The Ser169Leufs*9 mutation causes a frameshift mutation and premature stop codon. The mutation is in exon 4 and thus removes part of the F-BOX, all three CASH domains and the zinc-finger UBR region, thus it should act as a loss of function variation. No functional assays or variant evidence was provided.

Case: Individual 14, male, AOR= 9 years 10 months

CasePresentingHPOs: HP:0001263, HP:0001344, HP:0010864, HP:0001290, HP:0000739, HP:0000718, HP:0000637, HP:0000411, HP:0002019

CasePresentingHPOText: Began walking 4y.o., currently no speech. Noted as having NAD under abnormalities of the hand and feet.

CaseNOTHPOs: HP:0001250, HP:0002376, HP:0002360, HP:0000202, HP:0000924, HP:0002719

CaseNOTtextHPO:

CasePreviousTesting:

CaseGenotypingMethod: Trio-WES performed through the DDD consortium, 2017 PMID:PMID: 28135719.

Variant: g19:chr2: g.4804051 7C>T, c.2084-1G>A, p.(?) OR NM_001190274.1:c.2084-1G>A

CA ID: CA346763489

de novo

gnomAD: n/a

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VariantEvidence: The c.2084−1G>A mutation is most likely a splice site mutation. The mutation arises in exon 18 (Intron 18?), and likely would disrupt exon 18 splicing. Exon 18 is upstream of the third CASH domain, which regulates substrate recognition. No functional assays or variant evidence was provided, so I have downgraded the score.

Case: Individual 4, male, AOR= 8 yo

CasePresentingHPOs:  HP:0001518, HP:0004322, HP:0000252, HP:0001270, HP:0011344, HP:0002187HP:0000750, HP:0002069, HP:0002121, HP:0006829, HP:0100023, HP:0000735, HP:0000248, HP:0001357, HP:0000490, HP:0011229, HP:0000527, HP:0045025, HP:0003196, HP:0000414, HP:0000463, HP:0000288, HP:0000160, HP:0000219, HP:0000232, HP:0000307, HP:0000400, HP:0200055, HP:0001769, HP:0006045, HP:0004209, HP:0010610, HP:0001795, HP:0000193, HP:0003100, HP:0000938, HP:0002750, HP:0002205, HP:0000565, HP:0011968

CasePResentingHPOText: Subject began walking at 5 y.o. First words at 8 y.o. and noted as only having 2 words. Seizure onset at 3 y.o. with general tonic clonic seizures and absence. At 4 y.o. noted as having little social interaction, and intermittent hand flapping. Noted as having a feeding tube until age 8.

CaseNOTHPOs: HP:0002376, HP:0012443, HP:0002360

CasePreviousTesting: Affymetrix Cytogenetics 2.7 array testing was unremarkable.

CaseGenotypingMethod: Trio-WES. Testing also identified a de novo VUS in SMARCAD1 (NM_0011 28429.1):c hr4:g.9520 1881T>A, c.2563T>A, p.(Ser855Thr), this gene is associated with skin disease.

Variant: hg19:chr2: g.4804614 7G>C, c.1868C>G , p.(Thr623Arg) OR NM_001190274.1:c.1868C>G

CA ID: CA346764020

de novo Trio-WES performed so maternity and paternity could be investigated with this method.

gnomAD: n/a

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VariantEvidence: Thr623 is located in the second CASH domain of FBXO11, and is conserved across specieis. These domains are responsible for the substrate recognition. Pathogenicity algorithms showing varying predictions, from tolerated to damaging, thus indicating a VUS. No functional assays were performed to indicate the impact of the T623R mutation on FBXO11 function.

Case: Individual 11, male, AOR= 14 years

CasePresentingHPOs: HP:0001263, HP:0000750, HP:0001256, HP:0000752, HP:0001575, HP:0000276, HP:0000286, HP:0000278, HP:0000347, HP:0001182, HP:0001763, HP:0001852, HP:0011330, HP:0001382, HP:0002719, HP:0000540, HP:0000486, HP:0002967, HP:0001065, HP:0001724, HP:0010499, HP:0000243

CasePresentingHPOText: Began walking at 24 months old.

CaseNOTHPOs: HP:0001250, HP:0002376, HP:0012443,

CasePreviousTesting: Array-CGH (244K Agilent) normal, Fragile X syndrome (FMR1 Repeat analysis) normal, Loeys-Dietz syndrome (TGFBR1 and TGFBR2) normal and Marfan syndrome (FBN1) normal

CaseGenotypingMethod: WES (Agilent CRE and HiSeq 4000), searching for variants in FBXO11 after identification of variant in I13, Sanger confirmation to show de novo status and absence in parents. Sample identity confirmed.

Variant: hg19:chr2: g.4806002 0C>G, c.1042- 1G>C, p.(?) OR NM_001190274.1:c.1042- 1G>C(p.=)

CA ID: CA346765998

de novo splice site mutation.

gnomAD: n/a

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VariantEvidence: The c.1042-1G>C mutation is most likely a splice site mutation. The mutation arises in exon 9 (Intron 8), and likely would disrupt exon 9 transcription. Exon 9 does not transcirbe any of the funcitonal domains, but exon 10 comprises the NosD domain, which is 5' to the first CASH domain. No functional assays or variant evidence was provided, so I have downgraded the score.

Case: Individual 2, female, AOR= 8yo

CasePresentingHPOs: HP:0001263, HP:0000750, HP:0002342, HP:0007359, HP:0002500, HP:0001290, HP:0002360, HP:0000729, HP:0000739, HP:0025269, HP:0000490, HP:0001840, HP:0000486

CasePResentingHPOText: Began walking at 22 months, first words at 2yo,. Seizure onset at 7 yo and are focal, and occur nightly. Reduced white matter bulk on MRI. Referred to as having intoeing or pigeon-toed. Low APGAR scores, brief resuscitation required

CaseNOTHPOs: HP:0002376, HP:0000202, HP:0000924, HP:0002719,

CasePreviousTesting: ArrayCGH, Fragile X (FMR1), Angelman Syndrome (methylation & UBE3A), Rett syndrome (MECP2), Pitt-Hopkins Syndrome (TCF4), and extensive metabolic screening were all normal

CaseGenotypingMethod: Trio-WES performed through the DDD consortium, 2017 PMID:PMID: 28135719.

Variant: hg19:chr2: g.48066586T>A, c.414A>T, p.(Arg138Ser) or NM_001190274.1:c.414A>T

CA ID: CA346813374

de novo Trio-WES performed by DDD so maternity and paternity could be investigated with this method.

gnomAD: n/a

AddCaseInfo: Case was part of the DDD study 2017 PMID: 28135719,

VariantEvidence: Arg138 is located N-terminal to the F-box region of FBXO11, and is conserved across species. Pathogenicity algorithms showing varying predictions, from tolerated to damaging, thus indicating a VUS. No functional assays were performed to indicate the impact of the R138S mutation on FBXO11 function.

ExperimentName: Jeff mouse has FBXO11 Q491L mutation

NonHumanModel: mouse (mus musculus)

GeneAlteration: ENU (ethylnitrosourea) was used to induce random mutatgeneiss in the mouse (PMID: 10932191). Animals were screened based on the development of otitis media. Sequencing of the mouse genome FBXO11 gene, c. 1472A>T (. Q491L) that is located after the First CASH domain. The Gln at amino acid position 491 is conserved across several species.

HumanPhenotype: HP:0000175

ModelEvidence: HP:0000175

ModelPhenotype: The Jeff/ FBXO11 Q491L mice heterozygotes were originally shown to have increased susceptibility to developing otitis media (ear infections) (PMID: 10932191). Homozygote Jeff mouse mutants were shown to demonstrate perinatal lethality (death just after birth). this premature death was suspected to be due to respiratory problems as air was found in the stomach. Furthermore, the mice were shown to have eye abnormalities (upper eyelid open at birth) and cleft palate (hard or soft) and facial clefting (Fig. 2B). Of note, only the homozygotes Jeff mice showed the cleft palate, heterozygote Jeff mice were shown to have normal palates at 5, 13, 28, 56, and 120 days old.

ModelVariant: NM_001190274.1:c.1724A>T (p. Gln575Leu) consistent with ENST00000402508.5:c.1472A>T(p.Gln491Leu)

CA ID: CA346764369

Case: Fritzen-Individual 1, male, German, AOR= 14 y.o.

CasePresentingHPOs: HP:0000252, HP:0410034, HP:0008124, HP:0001156, HP:0001741, HP:0001263, HP:0001249, HP:0000752, HP:0000708, HP:0007018, HP:0011174, HP:0030891, HP:0012444, HP:0000582, HP:0000358, HP:0200055, HP:0001169, HP:0009381, HP:0001831, HP:0004691, HP:0001814,

CasePresenting HPOtext: Started talking at 18 months, started walking at 20 months. Deficits in expressive and receptive language. At 4 yo spoke first two word sentence. SON-R test at 5 indicated mild ID. K-ABC test at 8 yo revealed IQ of 53.

CaseNOTHPOs:

CasePreviousTesting: EEG, BERA, visual acuity test and routine cardiological check-ups were normal. Metabolic screening of urine (organic metabolites) was normal. Karotyping (blood lymphocytes), subtelomere screening, chromosomal microarray and Fragile X (FMR gene) screening were normal.

One homozygous mutation in ZNF717 and compound heterozygous mutations in EVPL were found, but ruled out based on too high of a frequency in control population of assertions of benign pathognicity.

CaseGenotypingMethod: Trio WES with parents.

Variant: NM_025133.4(FBXO11):c.190+1dup

Paper has written as NM_001190274.1:c.442 + 1T>G chr2:g.48066557dup

ClinVar ID: 559605

De novo Pathogenic, splice site variant, 1 submitter, no star

gnomAD: n/a

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VariantEvidence: No evidence to show the effect of the splice site mutation, although the authors note that it was "predicted unequivocally to result in aberrant splicing." Therefore, I have reduced the score.