HIVEP3
Basic information
Region (hg38): 1:41506365-42035925
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- HIVEP3-related_disorder (69 variants)
- not_provided (15 variants)
- Neurodevelopmental_disorder (1 variants)
- not_specified (1 variants)
- See_cases (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the HIVEP3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000024503.5. 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 | 31 | 13 | 44 | |||
missense | 11 | 14 | 32 | |||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 8 | 42 | 27 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
HIVEP3 | protein_coding | protein_coding | ENST00000372583 | 6 | 529561 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.906 | 0.0942 | 125639 | 0 | 109 | 125748 | 0.000434 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.17 | 1274 | 1.40e+3 | 0.912 | 0.0000839 | 15378 |
Missense in Polyphen | 373 | 526.24 | 0.70881 | 5946 | ||
Synonymous | -0.873 | 627 | 600 | 1.05 | 0.0000383 | 5206 |
Loss of Function | 6.34 | 15 | 73.7 | 0.203 | 0.00000435 | 880 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00106 | 0.00105 |
Ashkenazi Jewish | 0.00477 | 0.00477 |
East Asian | 0.00 | 0.00 |
Finnish | 0.0000924 | 0.0000924 |
European (Non-Finnish) | 0.000223 | 0.000220 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.000199 | 0.000196 |
Other | 0.000327 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Plays a role of transcription factor; binds to recognition signal sequences (Rss heptamer) for somatic recombination of immunoglobulin and T-cell receptor gene segments; Binds also to the kappa-B motif of gene such as S100A4, involved in cell progression and differentiation. Kappa-B motif is a gene regulatory element found in promoters and enhancers of genes involved in immunity, inflammation, and growth and that responds to viral antigens, mitogens, and cytokines. Involvement of HIVEP3 in cell growth is strengthened by the fact that its down- regulation promotes cell cycle progression with ultimate formation of multinucleated giant cells. Strongly inhibits TNF-alpha-induced NF-kappa-B activation; Interferes with nuclear factor NF-kappa-B by several mechanisms: as transcription factor, by competing for Kappa-B motif and by repressing transcription in the nucleus; through a non transcriptional process, by inhibiting nuclear translocation of RELA by association with TRAF2, an adapter molecule in the tumor necrosis factor signaling, which blocks the formation of IKK complex. Interaction with TRAF proteins inhibits both NF-Kappa-B-mediated and c-Jun N-terminal kinase/JNK-mediated responses that include apoptosis and proinflammatory cytokine gene expression. Positively regulates the expression of IL2 in T-cell. Essential regulator of adult bone formation. {ECO:0000269|PubMed:11161801}.;
- Pathway
- Transcriptional regulation by RUNX2;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Regulation of RUNX2 expression and activity
(Consensus)
Recessive Scores
- pRec
- 0.189
Intolerance Scores
- loftool
- 0.349
- rvis_EVS
- -0.51
- rvis_percentile_EVS
- 21.21
Haploinsufficiency Scores
- pHI
- 0.283
- hipred
- Y
- hipred_score
- 0.595
- ghis
- 0.468
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.684
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | High |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Hivep3
- Phenotype
- cellular phenotype; hematopoietic system phenotype; neoplasm; immune system phenotype; renal/urinary system phenotype; skeleton phenotype; limbs/digits/tail phenotype;
Gene ontology
- Biological process
- regulation of transcription by RNA polymerase II;skeletal muscle cell differentiation;positive regulation of transcription, DNA-templated
- Cellular component
- nucleus;cytoplasm
- Molecular function
- DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;metal ion binding