rs1182774429

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001127202.4(PCID2):​c.728C>T​(p.Ser243Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,158 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)

Consequence

PCID2
NM_001127202.4 missense

Scores

7
12

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.34
Variant links:
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]

Genome browser will be placed here

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=0.26238322).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PCID2NM_001127202.4 linkc.728C>T p.Ser243Phe missense_variant Exon 10 of 14 ENST00000337344.9 NP_001120674.1 Q5JVF3-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PCID2ENST00000337344.9 linkc.728C>T p.Ser243Phe missense_variant Exon 10 of 14 2 NM_001127202.4 ENSP00000337405.4 Q5JVF3-1
PCID2ENST00000375477.5 linkc.728C>T p.Ser243Phe missense_variant Exon 10 of 15 1 ENSP00000364626.1 Q5JVF3-1
PCID2ENST00000375479.6 linkc.728C>T p.Ser243Phe missense_variant Exon 10 of 15 2 ENSP00000364628.2 Q5JVF3-1
PCID2ENST00000375457.2 linkc.722C>T p.Ser241Phe missense_variant Exon 10 of 14 1 ENSP00000364606.2 Q5JVF3-2
PCID2ENST00000375459.5 linkc.722C>T p.Ser241Phe missense_variant Exon 10 of 15 2 ENSP00000364608.1 Q5JVF3-2

Frequencies

GnomAD3 genomes
AF:
0.00000657
AC:
1
AN:
152158
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
Cov.:
29
GnomAD4 genome
AF:
0.00000657
AC:
1
AN:
152158
Hom.:
0
Cov.:
33
AF XY:
0.0000135
AC XY:
1
AN XY:
74344
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.14
BayesDel_addAF
Benign
-0.0039
T
BayesDel_noAF
Benign
-0.24
CADD
Benign
19
DANN
Benign
0.97
DEOGEN2
Uncertain
0.57
.;D;D;D;.;.;.
Eigen
Benign
-0.64
Eigen_PC
Benign
-0.69
FATHMM_MKL
Uncertain
0.85
D
LIST_S2
Uncertain
0.96
D;.;.;D;.;.;D
M_CAP
Benign
0.034
D
MetaRNN
Benign
0.26
T;T;T;T;T;T;T
MetaSVM
Benign
-0.90
T
MutationAssessor
Benign
2.0
.;M;M;M;.;.;.
PrimateAI
Uncertain
0.59
T
PROVEAN
Uncertain
-3.3
.;D;D;D;D;D;D
REVEL
Benign
0.21
Sift
Uncertain
0.020
.;D;D;D;D;D;D
Sift4G
Uncertain
0.049
D;D;D;D;D;D;D
Polyphen
0.13
B;B;B;B;.;B;.
Vest4
0.44
MutPred
0.31
.;Loss of disorder (P = 0.0036);Loss of disorder (P = 0.0036);Loss of disorder (P = 0.0036);.;.;.;
MVP
0.25
MPC
0.81
ClinPred
0.71
D
GERP RS
0.22
Varity_R
0.22
gMVP
0.32

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1182774429; hg19: chr13-113835502; API