PAXIP1
PAX interacting protein 1
Basic information
Region (hg38): 7:154943687-155003124
Previous symbols: [ "PAXIP1L" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (69 variants)
- not_provided (3 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PAXIP1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000007349.4. 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 | 4 | |||||
| missense | 63 | 68 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 63 | 9 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PAXIP1 | protein_coding | protein_coding | ENST00000404141 | 21 | 59398 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 2.33e-9 | 124650 | 0 | 4 | 124654 | 0.0000160 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.28 | 332 | 548 | 0.605 | 0.0000300 | 6969 |
| Missense in Polyphen | 61 | 101.82 | 0.59909 | 1244 | ||
| Synonymous | 1.29 | 190 | 214 | 0.888 | 0.0000127 | 1946 |
| Loss of Function | 7.15 | 2 | 63.5 | 0.0315 | 0.00000314 | 731 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000357 | 0.0000357 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000556 | 0.0000556 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000177 | 0.0000177 |
| Middle Eastern | 0.0000556 | 0.0000556 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in DNA damage response and in transcriptional regulation through histone methyltransferase (HMT) complexes. Plays a role in early development. In DNA damage response is required for cell survival after ionizing radiation. In vitro shown to be involved in the homologous recombination mechanism for the repair of double-strand breaks (DSBs). Its localization to DNA damage foci requires RNF8 and UBE2N. Recruits TP53BP1 to DNA damage foci and, at least in particular repair processes, effective DNA damage response appears to require the association with TP53BP1 phosphorylated by ATM at 'Ser-25'. Together with TP53BP1 regulates ATM association. Proposed to recruit PAGR1 to sites of DNA damage and the PAGR1:PAXIP1 complex is required for cell survival in response to DNA damage; the function is probably independent of MLL-containing histone methyltransferase (HMT) complexes. However, this function has been questioned (By similarity). Promotes ubiquitination of PCNA following UV irradiation and may regulate recruitment of polymerase eta and RAD51 to chromatin after DNA damage. Proposed to be involved in transcriptional regulation by linking MLL-containing histone methyltransferase (HMT) complexes to gene promoters by interacting with promoter-bound transcription factors such as PAX2. Associates with gene promoters that are known to be regulated by KMT2D/MLL2. During immunoglobulin class switching in activated B-cells is involved in trimethylation of histone H3 at 'Lys-4' and in transcription initiation of downstream switch regions at the immunoglobulin heavy-chain (Igh) locus; this function appears to involve the recruitment of MLL-containing HMT complexes. Conflictingly, its function in transcriptional regulation during immunoglobulin class switching is reported to be independent of the MLL2/MLL3 complex (By similarity). {ECO:0000250|UniProtKB:Q6NZQ4, ECO:0000269|PubMed:14576432, ECO:0000269|PubMed:15456759, ECO:0000269|PubMed:17690115, ECO:0000269|PubMed:17925232, ECO:0000269|PubMed:18353733, ECO:0000269|PubMed:20088963, ECO:0000269|PubMed:23727112}.;
- Pathway
- DNA Repair;Nonhomologous End-Joining (NHEJ);DNA Double-Strand Break Repair
(Consensus)
Recessive Scores
- pRec
- 0.119
Intolerance Scores
- loftool
- 0.231
- rvis_EVS
- -0.49
- rvis_percentile_EVS
- 22.7
Haploinsufficiency Scores
- pHI
- 0.899
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.603
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.584
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Paxip1
- Phenotype
- embryo 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- positive regulation of histone H3-K36 methylation;vasculogenesis;double-strand break repair via nonhomologous end joining;DNA recombination;response to ionizing radiation;DNA damage response, signal transduction by p53 class mediator;positive regulation of protein ubiquitination;positive regulation of histone acetylation;endothelial cell migration;positive regulation of isotype switching;positive regulation of isotype switching to IgG isotypes;histone H3-K4 methylation;positive regulation of histone H3-K4 methylation;positive regulation of transcription initiation from RNA polymerase II promoter;adipose tissue development;chorion development;regulation of cell cycle G2/M phase transition;positive regulation of response to DNA damage stimulus
- Cellular component
- nucleus;nucleoplasm;chromosome;nuclear matrix;histone methyltransferase complex;MLL3/4 complex
- Molecular function
- protein binding