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Intellectual disability

Gene: PRPF8

Amber List (moderate evidence)

PRPF8 (pre-mRNA processing factor 8)
EnsemblGeneIds (GRCh38): ENSG00000174231
EnsemblGeneIds (GRCh37): ENSG00000174231
OMIM: 607300, Gene2Phenotype
PRPF8 is in 5 panels

2 reviews

Sarah Leigh (Genomics England Curator)

Green List (high evidence)

Associated with Retinitis pigmentosa 13 (OMIM:600059) in OMIM, but not with PRPF8-related developmental disorder (monoallelic) and as a both RD and IF Gen2Phen gene for PRPF8-related developmental disorder (monoallelic). PMID: 35543142 reports 14 PRPF8 variants in unrelated cases (12/14 variants were confirmed as de novo). Intellectual disability was observed in 13/14 of these cases and seizures were evident in 4/14 cases.
Created: 24 May 2022, 1:36 p.m. | Last Modified: 24 May 2022, 1:36 p.m.
Panel Version: 3.1587
Comment on phenotypes: Gen2Phen phenotype: PRPF8-related developmental disorder (monoallelic) in addition to Retinitis pigmentosa 13
Created: 24 May 2022, 1:30 p.m. | Last Modified: 24 May 2022, 1:30 p.m.
Panel Version: 3.1587
Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review.
Created: 24 May 2022, 1:28 p.m. | Last Modified: 24 May 2022, 1:28 p.m.
Panel Version: 3.1586

Konstantinos Varvagiannis (Other)

I don't know

A recent study suggests that heterozygous PRPF8 variants are associated with a syndromic form of DD/ID, in some cases epilepsy with heterogeneous other clinical findings. However the authors acknowledge that not all variants within their cohort may be pathogenic (5 VUSs using ACMG criteria) and that conclusive evidence may necessitate functional studies.

Heterozygous variants (typically clustering in exon 42) have been reported to cause a non-syndromic form of RP with variable expressivity and incomplete penetrance (Retinitis pigmentosa 13, MIM # 600059) .

Overall consider inclusion with amber rating.

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O'Grady et al. (2022 - PMID: 35543142) describe the phenotype of 14 unrelated individuals with heterozygous, mostly de novo, missense and pLoF variants in PRPF8.

Nearly all had some degree of global developmental delay or ID (13/14). 6/14 had a diagnosis of ASD. Seizures were reported in 4 or 5 subjects. Other features included short stature (6/14), abnormal gait, cardiac anomalies and somewhat overlapping facial features (11/14). Ages ranged from 4 - 19 years (median : 9y).

PRPF8 encodes a component of the spliceosomes which in turn are involved in removal of introns from mRNA precursors. The gene is ubiquitously expressed with expression within brain being highest in cerebral cortex, basal ganglia and cerebellum (Refs. provided).

Individuals were investigated with exome sequencing (12/14) or an autism/ID panel of >2500 genes (likely application of virtual panel on exome data).

13 individuals harbored a missense SNV and 1 further had a frameshift variant. In 12 individuals the variant had occurred de novo. 1 individual had inherited the variant from a possibly mosaic parent, while for 1 further a single parental sample was available.

PRPF8 is intolerant to both missense (Z = 8.28) and pLoF variants (pLI : 1). Variants in 5 individuals were formally classified as VUS while 2 variants were present in gnomAD.

Additional findings (CNVs/SNVs) were reported, in some cases possibly of relevance.

As the authors discuss, heterozygous pathogenic missense SNVs cause (and account for ~2-3% of) non-syndromic AD retinitis pigmentosa with variable expressivity and incomplete penetrance. Variants for this phenotype are typically missense - although nonsense ones have also been reported - clustering within ex42 (of 43) encoding the MPN domain (aa 2103-2335 / NP_006436) and weakening interaction with 2 other spliceosomal proteins.

Variants in the present study occurred throughout the gene. Although not universally assessed within the cohort, only one participant had RP (in this case variant within the MPN domain).

There were no variant studies performed.

Animal models: the authors cite a study by Graziotto et al (2011 - PMID: 20811066) where knock-in mice for a missense variant in ex42 displayed defects of the retinal pigment epithelium. A zebrafish ko model also cited (Keightley et al, 2013 - PMID: 23714367) displayed widespread apoptosis in brain and spinal cord.

The authors cite a previous bioinformatic study identifying PRPF8 as a major hub connecting gene-interaction networks for NDDs (Casanova et al, 2018 - PMID: 30420816) as well as 2 studies demonstrating enrichment of variants in individuals with NDDs compared to controls (da Silva Montenegro et al, 2020 - PMID: 31696658, Karczewski et al, 2020 - PMID: 32461654).
Sources: Literature
Created: 19 May 2022, 2:04 p.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

Phenotypes
Global developmental delay; Intellectual disability; Seizures; Autism; Retinitis pigmentosa 13, MIM # 600059

Publications

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Expert Review Amber
Phenotypes
  • PRPF8-related developmental disorder (monoallelic)
  • Retinitis pigmentosa 13, OMIM:600059
Tags
Q2_22_rating
OMIM
607300
Clinvar variants
Variants in PRPF8
Penetrance
unknown
Publications
Panels with this gene

History Filter Activity

24 May 2022, Gel status: 2

Set Phenotypes

Sarah Leigh (Genomics England Curator)

Phenotypes for gene: PRPF8 were changed from Global developmental delay; Intellectual disability; Seizures; Autism; Retinitis pigmentosa 13, OMIM:600059 to PRPF8-related developmental disorder (monoallelic); Retinitis pigmentosa 13, OMIM:600059

24 May 2022, Gel status: 2

Entity classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

Gene: prpf8 has been classified as Amber List (Moderate Evidence).

24 May 2022, Gel status: 0

Added Tag

Sarah Leigh (Genomics England Curator)

Tag Q2_22_rating tag was added to gene: PRPF8.

24 May 2022, Gel status: 0

Set Phenotypes

Sarah Leigh (Genomics England Curator)

Phenotypes for gene: PRPF8 were changed from Global developmental delay; Intellectual disability; Seizures; Autism; Retinitis pigmentosa 13, MIM # 600059 to Global developmental delay; Intellectual disability; Seizures; Autism; Retinitis pigmentosa 13, OMIM:600059

24 May 2022, Gel status: 0

Set publications

Sarah Leigh (Genomics England Curator)

Publications for gene: PRPF8 were set to 35543142

19 May 2022, Gel status: 0

Created, Added New Source, Set mode of inheritance, Set publications, Set Phenotypes, Set penetrance

Konstantinos Varvagiannis (Other)

gene: PRPF8 was added gene: PRPF8 was added to Intellectual disability. Sources: Literature Mode of inheritance for gene: PRPF8 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: PRPF8 were set to 35543142 Phenotypes for gene: PRPF8 were set to Global developmental delay; Intellectual disability; Seizures; Autism; Retinitis pigmentosa 13, MIM # 600059 Penetrance for gene: PRPF8 were set to unknown Review for gene: PRPF8 was set to AMBER