13-113196211-C-T
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001127202.4(PCID2):c.278G>A(p.Arg93Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000069 in 1,448,902 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Consequence
PCID2
NM_001127202.4 missense
NM_001127202.4 missense
Scores
1
6
12
Clinical Significance
Conservation
PhyloP100: 3.35
Genes affected
PCID2 (HGNC:25653): (PCI domain containing 2) This gene encodes a component of the TREX-2 complex (transcription and export complex 2), which regulates mRNA export from the nucleus. This protein regulates expression of Mad2 mitotic arrest deficient-like 1, a cell division checkpoint protein. This protein also interacts with and stabilizes Brca2 (breast cancer 2) protein. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.17188579).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCID2 | NM_001127202.4 | c.278G>A | p.Arg93Gln | missense_variant | 5/14 | ENST00000337344.9 | NP_001120674.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCID2 | ENST00000337344.9 | c.278G>A | p.Arg93Gln | missense_variant | 5/14 | 2 | NM_001127202.4 | ENSP00000337405.4 | ||
PCID2 | ENST00000375477.5 | c.278G>A | p.Arg93Gln | missense_variant | 5/15 | 1 | ENSP00000364626.1 | |||
PCID2 | ENST00000375479.6 | c.278G>A | p.Arg93Gln | missense_variant | 5/15 | 2 | ENSP00000364628.2 | |||
PCID2 | ENST00000375457.2 | c.272G>A | p.Arg91Gln | missense_variant | 5/14 | 1 | ENSP00000364606.2 | |||
PCID2 | ENST00000375459.5 | c.272G>A | p.Arg91Gln | missense_variant | 5/15 | 2 | ENSP00000364608.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 6.90e-7 AC: 1AN: 1448902Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 720792
GnomAD4 exome
AF:
AC:
1
AN:
1448902
Hom.:
Cov.:
28
AF XY:
AC XY:
0
AN XY:
720792
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
Bravo
AF:
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 26, 2023 | The c.278G>A (p.R93Q) alteration is located in exon 5 (coding exon 5) of the PCID2 gene. This alteration results from a G to A substitution at nucleotide position 278, causing the arginine (R) at amino acid position 93 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
.;T;T;T;.;.;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;.;.;T;.;.;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
.;M;M;M;.;.;.
PrimateAI
Benign
T
PROVEAN
Benign
.;N;N;N;N;N;N
REVEL
Benign
Sift
Uncertain
.;D;D;D;D;T;D
Sift4G
Benign
T;D;D;D;D;T;D
Polyphen
B;B;B;B;.;B;.
Vest4
MutPred
0.38
.;Gain of helix (P = 0.132);Gain of helix (P = 0.132);Gain of helix (P = 0.132);.;.;.;
MVP
MPC
0.20
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at