ZC3H10
Basic information
Region (hg38): 12:56118260-56127514
Previous symbols: [ "ZC3HDC10" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (39 variants)
- not_provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZC3H10 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000032786.3. 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 | 1 | |||||
| missense | 39 | 39 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 41 | 1 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ZC3H10 | protein_coding | protein_coding | ENST00000257940 | 1 | 4336 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.316 | 0.681 | 125741 | 0 | 3 | 125744 | 0.0000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.28 | 165 | 270 | 0.610 | 0.0000158 | 2789 |
| Missense in Polyphen | 29 | 69.175 | 0.41923 | 747 | ||
| Synonymous | -1.17 | 117 | 102 | 1.15 | 0.00000555 | 957 |
| Loss of Function | 2.53 | 3 | 12.7 | 0.236 | 9.77e-7 | 127 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000176 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Specific regulator of miRNA biogenesis. Binds, via the C3H1-type zinc finger domains, to the binding motif 5'-GCAGCGC-3' on microRNA pri-MIR143 and negatively regulates the processing to mature microRNA. {ECO:0000269|PubMed:28431233}.;
Recessive Scores
- pRec
- 0.108
Intolerance Scores
- loftool
- 0.0260
- rvis_EVS
- -0.18
- rvis_percentile_EVS
- 40.16
Haploinsufficiency Scores
- pHI
- 0.493
- hipred
- Y
- hipred_score
- 0.675
- ghis
- 0.523
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.999
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Zc3h10
- Phenotype
Gene ontology
- Biological process
- regulation of alternative mRNA splicing, via spliceosome;posttranscriptional regulation of gene expression;negative regulation of production of miRNAs involved in gene silencing by miRNA
- Cellular component
- nucleus;nucleoplasm;cytoplasm
- Molecular function
- RNA binding;protein binding;miRNA binding;metal ion binding