dn 5yearold female with developmental delay de novo Note These example CNVs have been created for educational purposes in order to ensure that each evidence type in the scoring matrices are utilized across the entire set no single CNV will necessarily cover all evidence types These a ID: 911569
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Slide1
Case Barr[GRCh37] 11p11.2 (45904399_46480747) x 1 (dn)
5-year-old female with developmental delay; de novo
Note: These example CNVs have been created for educational purposes in order to ensure that each evidence type in the scoring matrices are utilized across the entire set (no single CNV will necessarily cover all evidence types). These are not actual CNVs that have been observed in a laboratory setting. As such, please evaluate the coordinates as given, regardless of other considerations that may apply in the actual clinical laboratory setting. For example, if your CNV is below the size cutoff your laboratory uses on a daily basis, please disregard this for the sake of this exercise and evaluate the content within the provided coordinates. Assume that the CNV is technically valid.
Slide2Clinical Informationarr
[GRCh37] 11p11.2(45904399_46480747) x 1 (dn)5-year-old female with developmental delay; de novoUse the LOSS scoring metric
Slide3Section 1: Initial Assessment of Genomic Content
Would apply category 1A (contains protein-coding or other known functionally important elements), as this deletion includes several protein-coding genes.0 points; continue evaluation
Total: 0 points
Case B
Genes contained
Slide4Section 2: Overlap with Established/Predicted HI or Established Benign Genes/Genomic Regions
Case B overlaps a ClinGen curated pathogenic region
Part of the
Potocki
Shaffer region (HI Score of 3)
Slide5Zoom out to appreciate the context…
Our Case (Case B)
Curated
Potocki
Shaffer region
Both include
PHF21A
Slide6Potocki-Shaffer syndrome
ClinGen dosage curation results for the region: HI score = 3, TS score = 0 as of December 2013Loss of this region results in Potocki-Shaffer syndrome, a contiguous gene deletion syndromeCharacterized by: developmental delay, intellectual disability, multiple exostoses, parietal foramina, enlarged anterior fontanel, etc.
Loss of the
EXT2
gene is thought to cause the multiple exostoses phenotype
Loss of the
ALX4
gene is thought to cause the parietal foramina phenotype
Our case (Case B) does not involve either of these genes, but does overlap several genes at the proximal end of the curated region, including PHF21AUse Category 2B due to partial overlap; continue evaluation
Total: 0 points
Slide7HI Predictors
Since no points were awarded for overlapping with a known HI gene or genomic region, it would be appropriate to consider whether points should be awarded for HI predictors.2 genes in the interval meet current criteria (boxed in red).Remember, category 2H can only be scored ONCE, regardless of how many genes in the interval meet the criteria.
Total: 0.15 points
Slide8Section 3: Evaluation of Gene Number
There are 11 protein-coding genes in the interval (category 3A, 0 points).
Total: 0.15 points
Slide9Where to start?PHF21A has already been evaluated by ClinGen Dosage (though did not receive an HI score of 3 when originally evaluated)
logical starting point
Section 4: Detailed Evaluation of Genomic Content
Slide10https://dciw.clinicalgenome.org/clingen_gene.cgi?sym=PHF21A
Use this evidence as a starting point for Section 4.
Check for new evidence since May 2019.
Slide11Literature-based evidence from the ClinGen dosage evaluation
Hamanaka et al. (2019) (PMID:30487643)Describes 3 de novo putative LOF variants in PHF21A (NM_001101802.1) in individuals with non-specific neurodevelopmental phenotypes (variable intellectual disability, developmental delay, autistic features, epilepsy)
All 3 variants identified on trio exome sequencing (parental relationships can be considered confirmed); none of the variants are in gnomAD as of March 2020
Case 1: c.1220dupC (p.Glu408Argfs*3): 0.15 points
Case 2: c.1738C>T (p.Arg508*): This variant is in the penultimate exon, and is not expected to undergo nonsense mediated decay. No functional studies were performed to demonstrate the effect of this variant.
A subsequent paper reports this variant (
de novo
) in 2 additional probands (Kim et al., discussed later in the presentation). These authors note that this variant would remove the LZD2 functional domain; because of this, we will count each instance of this variant at a downgraded score of 0.075.
Case 3: c.657_658insAA (p.Pro220Asnfs*48):0.15 points
Total: 0.525 points
Slide12EuroEPINOMICS-RES Consortium et al. (2014) (PMID:25262651): Reported exome sequencing data of 356 trios with epileptic encephalopathies, infantile spasms, and/or Lennox
Gastaut syndromeParental relationships can be considered confirmedIn the supplemental material, the authors report a single individual (isnd38199aic1) with a de novo splice acceptor variant (a T>C change at genomic position 45958122 on chromosome 11 (GRCh37)).This individual was said to have infantile spasms; no additional information is available.
Because of lack of phenotypic information, consider this a non-specific phenotype
Variant not present in gnomAD as of March 2020
0.15 points
Literature-based evidence from the ClinGen dosage evaluation
Total: 0.675 points
Slide13Iossifov et al. 2014 (PMID:25363768):Reports exome sequencing data for more than 2500 families (proband with autism, unaffected sibling, and parents) from the Simons Simplex Collection
Parental relationships can be considered confirmedA single female proband with autism (Family ID 11339) was reported to have a de novo frameshift variant in PHF21A (11:45971023:CT:C)Variant not found in gnomAD as of March 2020No further clinical information is availableNon-specific phenotype
0.15 points
Literature-based evidence from the ClinGen dosage evaluation
Total: 0.825 points
Slide14Have there been any subsequent publications?
Yes! This paper came out in October 2019. The ClinGen dosage evaluation was completed in May 2019.
Slide15Kim et al. 2019 (PMID:31649809)
Describes 7 individuals with variants in PHF21A and variable neurodevelopmental phenotypes, including intellectual disability, developmental delay, autism spectrum disorders, and seizures.
Patient
Variant
Inheritance
Mode of Testing
Predicted Consequence
Score
1
c.1955delC (p.Pro652LeufsX104)
De novo
Trio exome
Frameshift; expected to result in elongated protein; not expected to result in NMD; expected to truncate intrinsically disordered region (IDR)0; unclear how this will affect protein; authors cannot r/o GOF or dominant negative
2
c.1285G>A (p.Gly429Ser)
De novo
Trio panel (520 genes)
Missense; thought to result in LOF due compromise in AT Hook: DNA interactions (protein modeling only)
0 (Missense variant, hypothesized but not demonstrated LOF)
3
c.1956delT (p.Pro652ProfsX104)
De novo
Trio exome
Frameshift; expected to result in elongated protein; not expected to result in NMD; expected to truncate IDR
0; unclear how this will affect protein; authors cannot r/o GOF or dominant negative
4
c.1738C>T (p.Arg580Ter)
De novo
Trio panel (520 genes)
Premature stop codon located 48 nucleotides upstream of the last exon-exon junction; not expected to undergo NMD, but is expected to be missing LZD2 functional domain
0.075 – downgrade due to NMD, but scoring due to missing
fx
domain
5
c.1471dupT (p.Cys491LeufsX81)
Not found in mother
Exome
Expected to result in truncated protein undergoing NMD; expected to be missing LZD2 and PHD finger domains
0 – Unknown inheritance, nonspecific phenotype
6
c.1738C>T (p.Arg580Ter)
De novo
Trio panel (520 genes)
Premature stop codon located 48 nucleotides upstream of the last exon-exon junction; not expected to undergo NMD, but is expected to be missing LZD2 functional domain
0.075 – downgrade due to NMD, but scoring due to missing
fx
domain
7
c.2024delA, p.Gln675ArgfsX81)
De novo
Trio exome
Frameshift; expected to result in elongated protein; not expected to result in NMD; expected to truncate IDR
0; unclear how this will affect protein; authors cannot r/o GOF or dominant negative
Total: 0.975 points
Slide16Additional supportive informationThere are 3 additional
de novo putative LOF variants in DECIPHER, each classified as “likely pathogenic”:379277: c.1147+1G>A301795: c.703C>T (p.Arg235Ter)292807: c.1855A>T (p.Lys619Ter) (last exon)Each proband is described as having variable neurodevelopmental disorder(s)Testing methodology and previous testing unknown
Unknown if parental relationships are confirmed
Slide17Additional supportive informationKim
et al. 2012 describe 3 patients with apparently balanced de novo translocations in which one breakpoint disrupts PHF21A. These individuals are noted to have neurodevelopmental and craniofacial phenotypes consistent with what has previously been reported in Potocki-Shaffer syndrome.For at least one of the subjects, the second breakpoint was found to be in a region “devoid of annotated genes.”
The authors also demonstrated that “zebrafish orthologs are…expressed in a manner consistent with a function in
neurofacial
and craniofacial development, and suppression of the [zebrafish ortholog] led to both craniofacial abnormalities and neuronal apoptosis.”
Slide18Additional supportive informationPorter
et al. 2018 (PMID:28571721):“RNA-Seq of PHF21A-deficient patient cells revealed 1,885 commonly misregulated genesPathway analysis showed downregulation of pathways relevant to learning and memory, including cAMP-mediated signaling
Reporter assays showed PHF21A is required for full induction of the cAMP-mediated transcriptional response
PHF21A-
deficient patient cells exhibited delayed transcription of immediate early genes following cAMP signaling.”
Slide19Section 5: Evaluation of Inheritance Pattern/Family History for Patient Being Studied
Our patient is said to have developmental delayThis is consistent with the expected phenotype, though relatively non-specificThe variant is said to be de novoSince original testing done by array CGH, confirmatory parental testing likely did not confirm both parental relationshipsUse category 5A (0.10 points)
Total: >1 point
Slide20ConclusionClassification: Pathogenic
Though the current ClinGen Dosage Sensitivity curation for the PHF21A gene is a 2, newer published information and additional supportive information suggest that loss of this gene results in variable neurodevelopmental phenotypes.This patient would not be expected to have the full Potocki-Shaffer phenotype (including multiple exostoses and parietal foramina) as the
EXT2
and
ALX4
genes are not involved.