rs202117698
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 4P and 4B. PVS1_StrongBS2
The ENST00000358450.8(PDE11A):c.20_21del(p.Arg7ThrfsTer30) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00288 in 1,614,002 control chromosomes in the GnomAD database, including 8 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.0026 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0029 ( 8 hom. )
Consequence
PDE11A
ENST00000358450.8 frameshift
ENST00000358450.8 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.86
Genes affected
PDE11A (HGNC:8773): (phosphodiesterase 11A) The 3',5'-cyclic nucleotides cAMP and cGMP function as second messengers in a wide variety of signal transduction pathways. 3',5'-cyclic nucleotide phosphodiesterases (PDEs) catalyze the hydrolysis of cAMP and cGMP to the corresponding 5'-monophosphates and provide a mechanism to downregulate cAMP and cGMP signaling. This gene encodes a member of the PDE protein superfamily. Mutations in this gene are a cause of Cushing disease and adrenocortical hyperplasia. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
CYCTP (HGNC:24424): (cytochrome c, testis, pseudogene) Predicted to enable heme binding activity. Predicted to act upstream of or within hydrogen peroxide metabolic process and positive regulation of intrinsic apoptotic signaling pathway. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PVS1
?
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant located near the start codon (<100nt), not predicted to undergo nonsense mediated mRNA decay. There are 6 pathogenic variants in the truncated region.
BS2
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High AC in GnomAd at 392 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDE11A | NM_001077197.2 | c.20_21del | p.Arg7ThrfsTer30 | frameshift_variant | 2/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDE11A | ENST00000358450.8 | c.20_21del | p.Arg7ThrfsTer30 | frameshift_variant | 2/21 | 1 | |||
CYCTP | ENST00000504253.1 | n.27_28del | non_coding_transcript_exon_variant | 1/3 |
Frequencies
GnomAD3 genomes ? AF: 0.00258 AC: 392AN: 152110Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00305 AC: 760AN: 249534Hom.: 1 AF XY: 0.00299 AC XY: 405AN XY: 135372
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GnomAD4 exome AF: 0.00291 AC: 4258AN: 1461774Hom.: 8 AF XY: 0.00286 AC XY: 2078AN XY: 727188
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GnomAD4 genome ? AF: 0.00258 AC: 392AN: 152228Hom.: 0 Cov.: 32 AF XY: 0.00292 AC XY: 217AN XY: 74422
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:1Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
Pigmented nodular adrenocortical disease, primary, 2 Pathogenic:1Uncertain:1
Uncertain significance, no assertion criteria provided | curation | Reproductive Health Research and Development, BGI Genomics | Jan 06, 2020 | NM_001077197.1:c.20_21delGA in PDE11A gene has an allele frequency of 0.013 in European (Finnish) subpopulation in the gnomAD database. This variant is expected to result in an absent or disrupted protein product. The current clinical and genetic evidence is not sufficient to establish whether loss-of-function variants in PDE11A cause disease. The available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. ACMG/AMP criteria applied: BS1. - |
Likely pathogenic, criteria provided, single submitter | reference population | Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center | Mar 18, 2016 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2024 | PDE11A: BS1, BS2 - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at