21-46411504-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006031.6(PCNT):c.5431C>T(p.Arg1811Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000087 in 1,609,314 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1811H) has been classified as Uncertain significance.
Frequency
Consequence
NM_006031.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCNT | NM_006031.6 | c.5431C>T | p.Arg1811Cys | missense_variant | 28/47 | ENST00000359568.10 | |
PCNT | NM_001315529.2 | c.5077C>T | p.Arg1693Cys | missense_variant | 28/47 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCNT | ENST00000359568.10 | c.5431C>T | p.Arg1811Cys | missense_variant | 28/47 | 1 | NM_006031.6 | P2 | |
PCNT | ENST00000480896.5 | c.5077C>T | p.Arg1693Cys | missense_variant | 28/47 | 1 | A2 | ||
PCNT | ENST00000695558.1 | c.5464C>T | p.Arg1822Cys | missense_variant | 29/48 | A2 | |||
PCNT | ENST00000703224.1 | c.*4674C>T | 3_prime_UTR_variant, NMD_transcript_variant | 30/49 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152146Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000427 AC: 1AN: 234328Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 128964
GnomAD4 exome AF: 0.00000824 AC: 12AN: 1457168Hom.: 0 Cov.: 34 AF XY: 0.0000110 AC XY: 8AN XY: 724798
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152146Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74314
ClinVar
Submissions by phenotype
Microcephalic osteodysplastic primordial dwarfism type II Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Feb 08, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at