ZC3HAV1
Basic information
Region (hg38): 7:139043515-139132122
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 ZC3HAV1 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 | 2 | |||||
missense | 43 | 49 | ||||
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 | 43 | 6 | 2 |
Variants in ZC3HAV1
This is a list of pathogenic ClinVar variants found in the ZC3HAV1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
7-139047672-A-C | not specified | Uncertain significance (Jan 22, 2024) | ||
7-139047707-T-C | not specified | Uncertain significance (Apr 27, 2022) | ||
7-139047833-C-G | not specified | Uncertain significance (May 24, 2024) | ||
7-139053504-G-A | not specified | Uncertain significance (Apr 26, 2023) | ||
7-139054073-T-C | not specified | Uncertain significance (Nov 15, 2021) | ||
7-139055234-A-C | not specified | Uncertain significance (Nov 07, 2022) | ||
7-139055248-C-T | not specified | Uncertain significance (Mar 01, 2023) | ||
7-139055249-G-A | not specified | Uncertain significance (Jan 23, 2023) | ||
7-139055274-C-T | Benign (Jun 29, 2018) | |||
7-139055275-G-A | not specified | Uncertain significance (Jan 06, 2023) | ||
7-139061079-A-G | not specified | Uncertain significance (Sep 06, 2022) | ||
7-139061112-T-C | not specified | Uncertain significance (Feb 13, 2024) | ||
7-139064903-G-A | not specified | Uncertain significance (Apr 11, 2023) | ||
7-139064935-G-A | not specified | Uncertain significance (Jan 09, 2024) | ||
7-139064963-A-G | not specified | Uncertain significance (Dec 16, 2023) | ||
7-139073917-G-A | not specified | Uncertain significance (Dec 01, 2022) | ||
7-139073929-T-A | not specified | Uncertain significance (Mar 14, 2023) | ||
7-139073959-G-C | not specified | Uncertain significance (Oct 17, 2023) | ||
7-139073980-G-A | not specified | Likely benign (Jan 10, 2023) | ||
7-139073988-A-C | not specified | Uncertain significance (Mar 20, 2024) | ||
7-139074035-GA-G | Benign (Jun 29, 2018) | |||
7-139076296-C-T | not specified | Likely benign (Dec 11, 2023) | ||
7-139076310-C-G | not specified | Likely benign (Feb 27, 2024) | ||
7-139076318-G-C | not specified | Uncertain significance (Jun 11, 2021) | ||
7-139076342-C-T | Benign (Feb 02, 2018) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
ZC3HAV1 | protein_coding | protein_coding | ENST00000242351 | 13 | 66200 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0000232 | 1.00 | 125729 | 0 | 19 | 125748 | 0.0000756 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.56 | 419 | 519 | 0.807 | 0.0000292 | 5912 |
Missense in Polyphen | 114 | 185.23 | 0.61545 | 2169 | ||
Synonymous | 0.238 | 200 | 204 | 0.979 | 0.0000123 | 1739 |
Loss of Function | 3.58 | 15 | 39.2 | 0.383 | 0.00000192 | 482 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000160 | 0.000159 |
Ashkenazi Jewish | 0.000101 | 0.0000992 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000895 | 0.0000879 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.000102 | 0.0000980 |
Other | 0.000165 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Antiviral protein which inhibits the replication of viruses by recruiting the cellular RNA degradation machineries to degrade the viral mRNAs. Binds to a ZAP-responsive element (ZRE) present in the target viral mRNA, recruits cellular poly(A)- specific ribonuclease PARN to remove the poly(A) tail, and the 3'- 5' exoribonuclease complex exosome to degrade the RNA body from the 3'-end. It also recruits the decapping complex DCP1-DCP2 through RNA helicase p72 (DDX17) to remove the cap structure of the viral mRNA to initiate its degradation from the 5'-end. Its target viruses belong to families which include retroviridae: human immunodeficiency virus type 1 (HIV-1), moloney and murine leukemia virus (MoMLV) and xenotropic MuLV-related virus (XMRV), filoviridae: ebola virus (EBOV) and marburg virus (MARV), togaviridae: sindbis virus (SINV) and Ross river virus (RRV). Specifically targets the multiply spliced but not unspliced or singly spliced HIV-1 mRNAs for degradation. Isoform 1 is a more potent viral inhibitor than isoform 2. Isoform 2 acts as a positive regulator of DDX58/RIG-I signaling resulting in activation of the downstream effector IRF3 leading to the expression of type I IFNs and IFN stimulated genes (ISGs). {ECO:0000269|PubMed:18225958, ECO:0000269|PubMed:21102435, ECO:0000269|PubMed:21876179, ECO:0000269|PubMed:22720057}.;
- Pathway
- Disease;Signaling by BRAF and RAF fusions;Oncogenic MAPK signaling;Diseases of signal transduction
(Consensus)
Recessive Scores
- pRec
- 0.0809
Intolerance Scores
- loftool
- 0.537
- rvis_EVS
- 0.72
- rvis_percentile_EVS
- 85.85
Haploinsufficiency Scores
- pHI
- 0.0770
- hipred
- N
- hipred_score
- 0.493
- ghis
- 0.432
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.588
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Zc3hav1
- Phenotype
- cellular phenotype;
Gene ontology
- Biological process
- response to virus;negative regulation of viral genome replication;innate immune response;defense response to virus;positive regulation of mRNA catabolic process;protein poly-ADP-ribosylation
- Cellular component
- nucleus;cytosol
- Molecular function
- RNA binding;NAD+ ADP-ribosyltransferase activity;protein binding;cadherin binding;metal ion binding;NAD+ binding