ZC3H13
Basic information
Region (hg38): 13:45954465-46052759
Previous symbols: [ "KIAA0853" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (184 variants)
- not_provided (3 variants)
- High_myopia (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZC3H13 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001330564.2. 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 | 4 | |||||
missense | 179 | 184 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 179 | 9 | 0 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
ZC3H13 | protein_coding | protein_coding | ENST00000282007 | 16 | 98295 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.00 | 2.72e-7 | 125725 | 0 | 23 | 125748 | 0.0000915 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.73 | 741 | 886 | 0.836 | 0.0000554 | 10227 |
Missense in Polyphen | 67 | 87.769 | 0.76337 | 920 | ||
Synonymous | 0.376 | 285 | 293 | 0.972 | 0.0000155 | 2984 |
Loss of Function | 8.16 | 14 | 104 | 0.135 | 0.00000933 | 920 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000244 | 0.000242 |
Ashkenazi Jewish | 0.000200 | 0.000198 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000108 | 0.0000967 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.000164 | 0.000131 |
Other | 0.000164 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Associated component of the WMM complex, a complex that mediates N6-methyladenosine (m6A) methylation of RNAs, a modification that plays a role in the efficiency of mRNA splicing and RNA processing (PubMed:29507755). Acts as a key regulator of m6A methylation by promoting m6A methylation of mRNAs at the 3'- UTR (By similarity). Controls embryonic stem cells (ESCs) pluripotency via its role in m6A methylation (By similarity). In the WMM complex, anchors component of the MACOM subcomplex in the nucleus (By similarity). Also required for bridging WTAP to the RNA-binding component RBM15 (RBM15 or RBM15B) (By similarity). {ECO:0000250|UniProtKB:E9Q784}.;
Recessive Scores
- pRec
- 0.102
Intolerance Scores
- loftool
- 0.407
- rvis_EVS
- -0.25
- rvis_percentile_EVS
- 35
Haploinsufficiency Scores
- pHI
- 0.477
- hipred
- Y
- hipred_score
- 0.571
- ghis
- 0.586
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.776
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Zc3h13
- Phenotype
Gene ontology
- Biological process
- mRNA processing;multicellular organism development;RNA splicing;mRNA methylation;regulation of stem cell population maintenance
- Cellular component
- nucleoplasm;nuclear speck;RNA N6-methyladenosine methyltransferase complex
- Molecular function
- RNA binding;protein binding;metal ion binding