rs1315359733
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_006031.6(PCNT):c.5482G>T(p.Glu1828Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,066 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_006031.6 stop_gained
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCNT | NM_006031.6 | c.5482G>T | p.Glu1828Ter | stop_gained | 28/47 | ENST00000359568.10 | |
PCNT | NM_001315529.2 | c.5128G>T | p.Glu1710Ter | stop_gained | 28/47 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCNT | ENST00000359568.10 | c.5482G>T | p.Glu1828Ter | stop_gained | 28/47 | 1 | NM_006031.6 | P2 | |
PCNT | ENST00000480896.5 | c.5128G>T | p.Glu1710Ter | stop_gained | 28/47 | 1 | A2 | ||
PCNT | ENST00000695558.1 | c.5515G>T | p.Glu1839Ter | stop_gained | 29/48 | A2 | |||
PCNT | ENST00000703224.1 | c.*4725G>T | 3_prime_UTR_variant, NMD_transcript_variant | 30/49 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460066Hom.: 0 Cov.: 34 AF XY: 0.00000138 AC XY: 1AN XY: 726356
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Jun 07, 2023 | For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 436277). This variant has not been reported in the literature in individuals affected with PCNT-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Glu1828*) in the PCNT gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PCNT are known to be pathogenic (PMID: 18174396, 22821869). - |
Microcephalic osteodysplastic primordial dwarfism type II Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | May 03, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at