Case B arr [GRCh37] 11p11.2 (45904399_46480747) x 1 ( - PowerPoint Presentation

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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.

Clinical Informationarr

[GRCh37] 11p11.2(45904399_46480747) x 1 (dn)5-year-old female with developmental delay; de novoUse the LOSS scoring metric

Section 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

Section 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)

Zoom out to appreciate the context…

Our Case (Case B)

Curated

Potocki

Shaffer region

Both include

PHF21A

Potocki-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

HI 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

Section 3: Evaluation of Gene Number

There are 11 protein-coding genes in the interval (category 3A, 0 points).

Total: 0.15 points

Where 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

https://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.

Literature-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

EuroEPINOMICS-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

Iossifov 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

Have there been any subsequent publications?

Yes! This paper came out in October 2019. The ClinGen dosage evaluation was completed in May 2019.

Kim 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

Additional 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

Additional 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.”

Additional 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.”

Section 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

ConclusionClassification: 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.