rs878853847
Positions:
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_000264.5(PTCH1):c.1615del(p.Glu539SerfsTer3) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Consequence
PTCH1
NM_000264.5 frameshift
NM_000264.5 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.58
Genes affected
PTCH1 (HGNC:9585): (patched 1) This gene encodes a member of the patched family of proteins and a component of the hedgehog signaling pathway. Hedgehog signaling is important in embryonic development and tumorigenesis. The encoded protein is the receptor for the secreted hedgehog ligands, which include sonic hedgehog, indian hedgehog and desert hedgehog. Following binding by one of the hedgehog ligands, the encoded protein is trafficked away from the primary cilium, relieving inhibition of the G-protein-coupled receptor smoothened, which results in activation of downstream signaling. Mutations of this gene have been associated with basal cell nevus syndrome and holoprosencephaly. [provided by RefSeq, Aug 2017]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 18 ACMG points.
PVS1
?
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 9-95476146-TC-T is Pathogenic according to our data. Variant chr9-95476146-TC-T is described in ClinVar as [Pathogenic]. Clinvar id is 237457.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-95476146-TC-T is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTCH1 | NM_000264.5 | c.1615del | p.Glu539SerfsTer3 | frameshift_variant | 12/24 | ENST00000331920.11 | |
PTCH1 | NM_001083603.3 | c.1612del | p.Glu538SerfsTer3 | frameshift_variant | 12/24 | ENST00000437951.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTCH1 | ENST00000331920.11 | c.1615del | p.Glu539SerfsTer3 | frameshift_variant | 12/24 | 5 | NM_000264.5 | A2 | |
PTCH1 | ENST00000437951.6 | c.1612del | p.Glu538SerfsTer3 | frameshift_variant | 12/24 | 5 | NM_001083603.3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Cov.: 34
GnomAD4 exome
Cov.:
34
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Gorlin syndrome Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Oct 04, 2020 | For these reasons, this variant has been classified as Pathogenic. Truncating variants in PTCH1 are known to be pathogenic. This particular truncation has been reported to segregate with Gorlin syndrome in a single family (PMID: 15459969). It was seen in 4 family members, with phenotypes of nevoid basal cell carcinoma, jaw cysts, and eye anomalies. This sequence change deletes 1 nucleotide from exon 12 of the PTCH1 mRNA (c.1615delG), causing a frameshift at codon 539. This creates a premature translational stop signal (p.Glu539Serfs*3) and is expected to result in an absent or disrupted protein product. - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Aug 19, 2016 | - - |
Computational scores
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Calibrated prediction
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at