ZC3HAV1

zinc finger CCCH-type containing, antiviral 1, the group of Zinc fingers CCCH-type|Poly(ADP-ribose) polymerases

Basic information

Region (hg38): 7:139043514-139132122

Links

ENSG00000105939 ∙ NCBI:56829 ∙ OMIM:607312 ∙ HGNC:23721 ∙ Uniprot:Q7Z2W4 ∙ 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 ZC3HAV1 gene.

• Inborn genetic diseases (34 variants)
• not provided (3 variants)

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	2
missense			30	4		34
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	30	4	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)
7-139053504-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)
7-139074035-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)
7-139076363-C-T		not specified	Uncertain significance (May 04, 2023)
7-139078627-T-C		not specified	Uncertain significance (Nov 08, 2022)

GnomAD

Source: gnomAD

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: dbNSFP

• 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