Table 2.

Details of the 9/36 Individuals that were Resolved by Bioinformatics Reanalyses of pre-UDN ES Data and Phenotyping

Individual number and Phenotype		Pre-UDN ES	Reason for Pre-UDN negative ES#		Duke/Columbia Bioinformatics Reanalyses and Annotation of Gene/Variants	Certainty of Diagnosis and Details
1	14 year-old Caucasian female with growth failure, metaphyseal dysplasia and thrombocytopenia	Research	Variability in Laboratory Reporting (Prioritization)	Research lab identified variant, did not prioritize due to focus on de novos	EFL1 c.379A>G p.T127A Tier 1 newly homozygous	Certain Shwachman-Diamond-like syndrome
2	18 year-old Caucasian female with hemiplegic migraine, hypotonia, ataxia, cerebellar atrophy and severe intellectual disability	Research	Analytical Approach (Technical limitation)	Not detected by research laboratory due to unknown reasons	CACNA1A c.4055G>T p.R1352L Tier 1 de novo in HZ [E] and HZ [OMIM]. Variant previously in ClinVar	Certain Epileptic encephalopathy, early infantile, 42 (MIM#617106)
3	14 year-old Caucasian male with renal failure due to nephronophthisis, retinal dystrophy and cerebellar ataxia	Research	Analytical Approach (Technical limitation of ES in CNV detection)	Homozygous deletion of NPHP1 gene not easily amenable to ES	NPHP1* Homozygous deletion CNV calling with GATK4 on exome	Certain Nephronophthisis, familial juvenile (MIM#256100)
4	8 month-old Caucasian male with congenital hypotonia, muscle weakness, fine tremor, laryngomalacia and motor delay	Commercial	Variability in Laboratory Reporting (Interpretation)	Not reported by clinical lab since phenotype not thought to be a good fit due to lack of arthrogryposis	MYBPC1* c.776T>C p.L259P Tier 1 de novo in HZ [OMIM].	Highly Likely Phenotypic expansion of Distal Arthrogryposis, Type 1B (MIM#614335); three other similar patients identified, all with congenital hypotonia, tremors that have improved over time, with normal cognition
5	20 month-old Caucasian male with infantile spasms, microcephaly, lamellar cataracts, failure to thrive and global developmental delay	Commercial	Knowledge Gap (gene-disease relationship not established)	Reported as candidate gene with VUS	NACC1** c.892C>T p.R298W Tier 1 de novo in HZ [E]	Certain Neurodevelopmental disorder with epilepsy, cataracts, feeding difficulties and delayed brain myelination (MIM#617393)
6	16 month-old Caucasian female with axonal motor neuron disease and cerebellar atrophy	Commercial	Knowledge Gap (gene-disease relationship not established)	Reported as candidate gene with VUS	AGTPBP1*** c.2492-1G>T IVS16-1G>T c.2892delC p.Y964X LoF variants in LoF depleted gene	Certain Infantile-onset degeneration of central and peripheral nervous systems; nine other patients identified
7	6 year-old Caucasian male with developmental delay, hypotonia, followed by progressive neurological regression	Research	Unknown reasons	Not reported for unknown reasons	IRF2BPL*** c.514 G>T p.E172X Tier 1 de novo LoF in LoF depleted gene	Highly Likely IRF2BPL associated neurodegenerative disorder; six patients identified with similar phenotypes
8	7 year-old Caucasian female with epilepsy, hypotonia, profound intellectual disability, cortical visual impairment Subsequently found to have prolonged QT interval	Commercial	Variability in Laboratory Reporting (Interpretation)	Not reported by clinical lab since phenotype not thought to be a good fit, due to lack of syndactyly and electrocardiographic abnormalities	CACNA1C* c.4087G>T p.V1363L Tier 1 de novo in HZ [E] and HZ [OMIM].	Highly Likely Timothy syndrome (MIM#601005); diagnosis on patient supported by additional phenotyping with ECG and Holter monitoring. Three other similar patients identified who presented with epilepsy, intellectual disability, no syndactyly and on further investigation 2/3 had long QT interval, thus representing likely phenotypic expansion of disorder (electrographic investigations pending in third patient)
9	10 year-old Caucasian female with developmental delay, microcephaly, hypotonia, minor dysmorphic features, conductive hearing loss	Research	Knowledge Gap (gene-disease relationship not established)	Not reported due to lack of disease association	HNRNPK* c.173T>C p.I58T Tier 1 de novo	Tentative Au-Kline syndrome (MIM#616580). Functional studies of variant pending

^#Reasons for negative WES classified into Analytical Approach differences, Knowledge Gap and Variability in Laboratory Reporting, with specific reasons under each category being provided whenever available

^*WGS through the UDN also performed, but variant not reported

^**Now established to be new disease associated gene

^***Candidate gene pursued with further clinical and functional studies, resulting in multiple affected patients and enough evidence to publish as new disease associated gene

HZ= Hot zone variant

E= Essential gene in mouse