HIVEP1
Basic information
Region (hg38): 6:12008762-12164999
Previous symbols: [ "ZNF40" ]
Links
Phenotypes
GenCC
Source:
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 HIVEP1 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 | 16 | 23 | ||||
missense | 151 | 21 | 16 | 188 | ||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 1 | 1 | 2 | |||
non coding | 0 | |||||
Total | 0 | 0 | 151 | 37 | 23 |
Variants in HIVEP1
This is a list of pathogenic ClinVar variants found in the HIVEP1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
6-12015643-A-G | Likely benign (Apr 01, 2022) | |||
6-12015666-G-A | not specified | Uncertain significance (Sep 27, 2022) | ||
6-12089215-T-G | not specified | Uncertain significance (Mar 14, 2023) | ||
6-12119955-G-A | not specified | Uncertain significance (Nov 25, 2024) | ||
6-12120048-G-A | not specified | Likely benign (Jun 24, 2022) | ||
6-12120057-C-T | Likely benign (Jul 15, 2018) | |||
6-12120073-C-G | not specified | Uncertain significance (Jan 29, 2024) | ||
6-12120093-A-C | not specified | Uncertain significance (Dec 26, 2023) | ||
6-12120151-T-C | not specified | Likely benign (Dec 10, 2024) | ||
6-12120195-C-A | not specified | Uncertain significance (Nov 25, 2024) | ||
6-12120204-C-G | not specified | Uncertain significance (Oct 04, 2022) | ||
6-12120226-G-A | not specified | Uncertain significance (Oct 11, 2023) | ||
6-12120275-T-A | not specified | Uncertain significance (Feb 10, 2022) | ||
6-12120303-A-G | Benign (Dec 31, 2019) | |||
6-12120327-G-A | not specified | Uncertain significance (Nov 08, 2022) | ||
6-12120336-T-C | HIVEP1-related disorder • not specified | Uncertain significance (Aug 28, 2024) | ||
6-12120419-C-T | Benign (Dec 31, 2019) | |||
6-12120431-A-G | Likely benign (Jun 01, 2022) | |||
6-12120516-A-G | not specified | Uncertain significance (Jul 09, 2021) | ||
6-12120573-A-C | HIVEP1-related disorder | Uncertain significance (Sep 03, 2023) | ||
6-12120573-A-G | not specified | Uncertain significance (May 02, 2024) | ||
6-12120679-A-G | not specified | Uncertain significance (Aug 27, 2024) | ||
6-12120691-A-G | not specified | Uncertain significance (Jun 16, 2023) | ||
6-12120700-C-T | not specified | Uncertain significance (May 20, 2024) | ||
6-12120710-A-G | HIVEP1-related disorder | Likely benign (Aug 29, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
HIVEP1 | protein_coding | protein_coding | ENST00000379388 | 8 | 156238 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.00 | 2.52e-8 | 124789 | 0 | 19 | 124808 | 0.0000761 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.328 | 1409 | 1.44e+3 | 0.976 | 0.0000774 | 17710 |
Missense in Polyphen | 338 | 464.48 | 0.7277 | 5735 | ||
Synonymous | -0.358 | 587 | 576 | 1.02 | 0.0000346 | 5545 |
Loss of Function | 7.66 | 8 | 83.6 | 0.0957 | 0.00000463 | 1074 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000123 | 0.000122 |
Ashkenazi Jewish | 0.000199 | 0.000199 |
East Asian | 0.000111 | 0.000111 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000885 | 0.0000883 |
Middle Eastern | 0.000111 | 0.000111 |
South Asian | 0.0000659 | 0.0000654 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: This protein specifically binds to the DNA sequence 5'- GGGACTTTCC-3' which is found in the enhancer elements of numerous viral promoters such as those of SV40, CMV, or HIV-1. In addition, related sequences are found in the enhancer elements of a number of cellular promoters, including those of the class I MHC, interleukin-2 receptor, and interferon-beta genes. It may act in T-cell activation. Involved in activating HIV-1 gene expression. Isoform 2 and isoform 3 also bind to the IPCS (IRF1 and p53 common sequence) DNA sequence in the promoter region of interferon regulatory factor 1 and p53 genes and are involved in transcription regulation of these genes. Isoform 2 does not activate HIV-1 gene expression. Isoform 2 and isoform 3 may be involved in apoptosis.;
Intolerance Scores
- loftool
- 0.339
- rvis_EVS
- 1.22
- rvis_percentile_EVS
- 93.09
Haploinsufficiency Scores
- pHI
- 0.184
- hipred
- Y
- hipred_score
- 0.538
- ghis
- 0.502
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.721
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | High |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Hivep1
- Phenotype
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II
- Cellular component
- nucleus;nucleoplasm;mitochondrion;nuclear body
- Molecular function
- RNA polymerase II distal enhancer sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;metal ion binding