PSIP1

PC4 and SRSF1 interacting protein 1, the group of Heparin binding growth factor family

Basic information

Region (hg38): 9:15464065-15510995

Previous symbols: [ "PSIP2" ]

Links

ENSG00000164985 ∙ NCBI:11168 ∙ OMIM:603620 ∙ HGNC:9527 ∙ Uniprot:O75475 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PSIP1 gene.

• Inborn genetic diseases (15 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.

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	1	2
missense			16	1	2	19
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	16	2	3

Variants in PSIP1

This is a list of pathogenic ClinVar variants found in the PSIP1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
9-15465534-T-C		not specified	Uncertain significance (Feb 16, 2023)
9-15465565-C-G		not specified	Uncertain significance (Mar 01, 2023)
9-15465567-C-G		not specified	Uncertain significance (Jul 19, 2023)
9-15465569-T-C		not specified	Uncertain significance (Jan 04, 2024)
9-15466784-T-G		not specified	Uncertain significance (Feb 21, 2024)
9-15466806-G-T		not specified	Uncertain significance (Jun 01, 2023)
9-15466830-C-G			Likely benign (Jun 21, 2018)
9-15466844-T-C		not specified	Uncertain significance (Jul 12, 2023)
9-15466848-G-C			Benign (Sep 09, 2018)
9-15468635-T-A			Benign (Dec 31, 2019)
9-15468830-T-G		not specified	Uncertain significance (Jan 08, 2024)
9-15469011-C-A		not specified	Uncertain significance (Jan 06, 2023)
9-15469944-T-G		not specified	Uncertain significance (Jun 16, 2023)
9-15469976-C-T		not specified	Uncertain significance (Aug 21, 2023)
9-15472680-T-G		not specified	Uncertain significance (Jul 06, 2021)
9-15474024-A-T		not specified	Uncertain significance (Aug 02, 2021)
9-15474121-T-C		not specified	Uncertain significance (Sep 01, 2021)
9-15474125-G-T		not specified	Uncertain significance (Feb 05, 2024)
9-15478484-T-G		not specified	Uncertain significance (Dec 13, 2022)
9-15478502-G-C		not specified	Uncertain significance (Jun 21, 2022)
9-15479671-T-G		not specified	Uncertain significance (Oct 26, 2022)
9-15486060-A-G			Benign (Mar 02, 2018)
9-15486872-A-C			Uncertain significance (Nov 01, 2022)
9-15486913-T-C		not specified	Uncertain significance (Jun 29, 2023)
9-15510109-T-C			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

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: dbNSFP

• 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