rs202221024
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_006031.6(PCNT):c.4078C>T(p.Arg1360Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000342 in 1,607,556 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1360H) has been classified as Uncertain significance.
Frequency
Consequence
NM_006031.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCNT | NM_006031.6 | c.4078C>T | p.Arg1360Cys | missense_variant | 21/47 | ENST00000359568.10 | |
PCNT | NM_001315529.2 | c.3724C>T | p.Arg1242Cys | missense_variant | 21/47 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCNT | ENST00000359568.10 | c.4078C>T | p.Arg1360Cys | missense_variant | 21/47 | 1 | NM_006031.6 | P2 | |
PCNT | ENST00000480896.5 | c.3724C>T | p.Arg1242Cys | missense_variant | 21/47 | 1 | A2 | ||
PCNT | ENST00000695558.1 | c.4078C>T | p.Arg1360Cys | missense_variant | 21/48 | A2 | |||
PCNT | ENST00000703224.1 | c.*3321C>T | 3_prime_UTR_variant, NMD_transcript_variant | 23/49 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 152172Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000145 AC: 34AN: 234690Hom.: 0 AF XY: 0.000134 AC XY: 17AN XY: 126920
GnomAD4 exome AF: 0.0000247 AC: 36AN: 1455268Hom.: 0 Cov.: 32 AF XY: 0.0000207 AC XY: 15AN XY: 723024
GnomAD4 genome ? AF: 0.000125 AC: 19AN: 152288Hom.: 0 Cov.: 33 AF XY: 0.000175 AC XY: 13AN XY: 74454
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 22, 2016 | - - |
Microcephalic osteodysplastic primordial dwarfism type II Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 31, 2018 | - - |
PCNT-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 28, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at