rs1555956600
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_006031.6(PCNT):c.1975dup(p.Asp659GlyfsTer18) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000041 in 1,461,830 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. D657D) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_006031.6 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCNT | NM_006031.6 | c.1975dup | p.Asp659GlyfsTer18 | frameshift_variant | 13/47 | ENST00000359568.10 | |
PCNT | NM_001315529.2 | c.1621dup | p.Asp541GlyfsTer18 | frameshift_variant | 13/47 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCNT | ENST00000359568.10 | c.1975dup | p.Asp659GlyfsTer18 | frameshift_variant | 13/47 | 1 | NM_006031.6 | P2 |
Frequencies
GnomAD3 genomes ? Cov.: 34
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461830Hom.: 0 Cov.: 32 AF XY: 0.00000688 AC XY: 5AN XY: 727222
GnomAD4 genome ? Cov.: 34
ClinVar
Submissions by phenotype
Microcephalic osteodysplastic primordial dwarfism type II Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 30, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at