GeneBe

ZC3H13

zinc finger CCCH-type containing 13, the group of Zinc fingers CCCH-type|WTAP complex

Basic information

Region (hg38): 13:45954465-46052759

Previous symbols: [ "KIAA0853" ]

Links

ENSG00000123200 ∙ NCBI:23091 ∙ OMIM:616453 ∙ HGNC:20368 ∙ Uniprot:Q5T200 ∙ 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 ZC3H13 gene.

  • 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.

EffectPLPVUSLBBSum
synonymous
4
clinvar
 4
missense
179
clinvar
5
clinvar
 184
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 179 9 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ZC3H13protein_codingprotein_codingENST00000282007 1698295
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
1.002.72e-71257250231257480.0000915
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.737418860.8360.000055410227
Missense in Polyphen6787.7690.76337920
Synonymous0.3762852930.9720.00001552984
Loss of Function8.16141040.1350.00000933920

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002440.000242
Ashkenazi Jewish0.0002000.000198
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.0001080.0000967
Middle Eastern0.000.00
South Asian0.0001640.000131
Other0.0001640.000163

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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