PCID2
PCI domain containing 2, the group of Transcription and export complex 2
Basic information
Region (hg38): 13:113177536-113208715
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCID2 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 9 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 8 | 1 | 1 |
Variants in PCID2
This is a list of pathogenic ClinVar variants found in the PCID2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 13-113178208-G-A | not specified | Uncertain significance (May 09, 2024) | ||
| 13-113178291-C-T | Benign (Dec 31, 2019) | |||
| 13-113180007-G-A | not specified | Uncertain significance (Oct 25, 2024) | ||
| 13-113180020-G-T | not specified | Likely benign (Sep 12, 2023) | ||
| 13-113180162-C-T | not specified | Uncertain significance (Jan 02, 2024) | ||
| 13-113181168-T-C | not specified | Uncertain significance (Dec 27, 2022) | ||
| 13-113181188-G-C | not specified | Uncertain significance (Jun 06, 2023) | ||
| 13-113181191-C-T | not specified | Uncertain significance (Jul 05, 2024) | ||
| 13-113181192-G-A | not specified | Uncertain significance (Sep 10, 2024) | ||
| 13-113181222-A-C | not specified | Uncertain significance (Apr 19, 2024) | ||
| 13-113184358-C-T | not specified | Uncertain significance (Jun 22, 2021) | ||
| 13-113190934-C-A | Benign (May 14, 2018) | |||
| 13-113190938-A-C | not specified | Uncertain significance (Jul 02, 2024) | ||
| 13-113190955-C-A | not specified | Uncertain significance (Aug 14, 2024) | ||
| 13-113196209-C-T | not specified | Uncertain significance (Sep 22, 2022) | ||
| 13-113196211-C-T | not specified | Uncertain significance (Sep 26, 2023) | ||
| 13-113197196-C-T | not specified | Uncertain significance (Oct 05, 2023) | ||
| 13-113200443-G-A | not specified | Uncertain significance (Aug 19, 2024) | ||
| 13-113200510-C-T | not specified | Uncertain significance (Apr 17, 2023) | ||
| 13-113208624-A-G | not specified | Uncertain significance (Nov 14, 2024) | ||
| 13-113208627-T-G | not specified | Uncertain significance (Nov 11, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PCID2 | protein_coding | protein_coding | ENST00000246505 | 14 | 31139 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 5.27e-13 | 0.343 | 125694 | 0 | 54 | 125748 | 0.000215 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.56 | 186 | 256 | 0.726 | 0.0000142 | 2993 |
| Missense in Polyphen | 33 | 53.917 | 0.61205 | 649 | ||
| Synonymous | 0.398 | 96 | 101 | 0.950 | 0.00000634 | 822 |
| Loss of Function | 1.22 | 23 | 30.2 | 0.761 | 0.00000162 | 349 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000177 | 0.000177 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000163 | 0.000163 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000345 | 0.000343 |
| Middle Eastern | 0.000163 | 0.000163 |
| South Asian | 0.000197 | 0.000196 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Required for B-cell survival through the regulation of the expression of cell-cycle checkpoint MAD2L1 protein during B cell differentiation (By similarity). Component of the TREX-2 complex (transcription and export complex 2), composed of at least ENY2, GANP, PCID2, SEM1, and either centrin CETN2 or CETN3 (PubMed:22307388). The TREX-2 complex functions in docking export- competent ribonucleoprotein particles (mRNPs) to the nuclear entrance of the nuclear pore complex (nuclear basket). TREX-2 participates in mRNA export and accurate chromatin positioning in the nucleus by tethering genes to the nuclear periphery. Binds and stabilizes BRCA2 and is thus involved in the control of R-loop- associated DNA damage and transcription-associated genomic instability. R-loop accumulation does not increase in PCID2- depleted cells. {ECO:0000250, ECO:0000269|PubMed:22307388, ECO:0000269|PubMed:24896180}.;
Recessive Scores
- pRec
- 0.106
Intolerance Scores
- loftool
- 0.262
- rvis_EVS
- -0.6
- rvis_percentile_EVS
- 17.75
Haploinsufficiency Scores
- pHI
- 0.517
- hipred
- Y
- hipred_score
- 0.721
- ghis
- 0.665
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.940
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pcid2
- Phenotype
- immune system phenotype; digestive/alimentary phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cellular phenotype; endocrine/exocrine gland phenotype;
Gene ontology
- Biological process
- posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery;transcription elongation from RNA polymerase II promoter;poly(A)+ mRNA export from nucleus;negative regulation of apoptotic process;regulation of mRNA stability;positive regulation of B cell differentiation;positive regulation of transcription, DNA-templated;spleen development;nuclear retention of pre-mRNA at the site of transcription;positive regulation of mitotic cell cycle spindle assembly checkpoint;negative regulation of cysteine-type endopeptidase activity
- Cellular component
- cellular_component;transcriptionally active chromatin;transcription export complex 2
- Molecular function
- double-stranded DNA binding;RNA binding;protein binding