PSIP1
PC4 and SRSF1 interacting protein 1, the group of Heparin binding growth factor family
Basic information
Region (hg38): 9:15464066-15510995
Previous symbols: [ "PSIP2" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (50 variants)
- not_provided (7 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSIP1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000033222.5. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | |||||
| missense | 51 | 54 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 51 | 2 | 3 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PSIP1 | protein_coding | protein_coding | ENST00000380733 | 15 | 46954 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.997 | 0.00332 | 125727 | 0 | 21 | 125748 | 0.0000835 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.106 | 262 | 267 | 0.982 | 0.0000128 | 3512 |
| Missense in Polyphen | 97 | 121.5 | 0.79838 | 1645 | ||
| Synonymous | -2.26 | 116 | 88.8 | 1.31 | 0.00000453 | 906 |
| Loss of Function | 4.81 | 4 | 34.4 | 0.116 | 0.00000195 | 418 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000885 | 0.0000885 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.000133 | 0.000132 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000659 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcriptional coactivator involved in neuroepithelial stem cell differentiation and neurogenesis. Involved in particular in lens epithelial cell gene regulation and stress responses. May play an important role in lens epithelial to fiber cell terminal differentiation. May play a protective role during stress-induced apoptosis. Isoform 2 is a more general and stronger transcriptional coactivator. Isoform 2 may also act as an adapter to coordinate pre-mRNA splicing. Cellular cofactor for lentiviral integration. {ECO:0000269|PubMed:15642333}.;
- Disease
- DISEASE: Note=A chromosomal aberration involving PSIP1 is associated with pediatric acute myeloid leukemia (AML) with intermediate characteristics between M2-M3 French-American-British (FAB) subtypes. Translocation t(9;11)(p22;p15) with NUP98. The chimeric transcript is an in-frame fusion of NUP98 exon 8 to PSIP1 exon 4. {ECO:0000269|PubMed:15725483}.;
- Pathway
- Disease;HIV Life Cycle;Host Interactions of HIV factors;HIV Infection;Vpr-mediated nuclear import of PICs;2-LTR circle formation;Infectious disease;APOBEC3G mediated resistance to HIV-1 infection;Interactions of Vpr with host cellular proteins;Integration of viral DNA into host genomic DNA;Autointegration results in viral DNA circles;Integration of provirus;Early Phase of HIV Life Cycle
(Consensus)
Recessive Scores
- pRec
- 0.152
Intolerance Scores
- loftool
- 0.715
- rvis_EVS
- -0.05
- rvis_percentile_EVS
- 50.22
Haploinsufficiency Scores
- pHI
- 0.990
- hipred
- Y
- hipred_score
- 0.792
- ghis
- 0.640
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.992
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Psip1
- Phenotype
- cellular phenotype; craniofacial phenotype; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; immune system phenotype; vision/eye phenotype; hematopoietic system phenotype; reproductive system phenotype; normal 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);
Gene ontology
- Biological process
- mRNA 5'-splice site recognition;response to oxidative stress;response to heat;nuclear transport;establishment of integrated proviral latency
- Cellular component
- nucleoplasm;cytosol;transcriptionally active chromatin
- Molecular function
- RNA binding;protein binding;supercoiled DNA binding