ZC3H11A
protein-codingzinc finger CCCH-type containing 11A, the group of Transcription and export complex 1 subunits|Zinc fingers CCCH-type
Gene summary
Enables RNA binding activity. Involved in poly(A)+ mRNA export from nucleus. Located in transcription export complex. [provided by Alliance of Genome Resources, Jul 2025]
- ZC3HDC11A
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~59.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to ZC3H11A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001376342.1. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 2 | 1 | 4 | ||
| missense | 94 | 9 | 103 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 6 | 6 | ||||
| Total | 0 | 0 | 103 | 11 | 1 | 115 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001363271.1 | 16 | MANE Select | |
| Ensembl | ENSP00000356179.1 | 16 | MANE Select | |
| RefSeq | NP_001306167.1 | 16 | Standard | |
| RefSeq | NP_001306168.1 | 16 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Gene expression (Transcription)
- RNA Polymerase II Transcription
- Metabolism of RNA
- Cleavage of Growing Transcript in the Termination Region
- RNA Polymerase II Transcription Termination
Biological Process
- regulation of transcription by RNA polymerase II
- RNA export from nucleus
- mRNA export from nucleus
- poly(A)+ mRNA export from nucleus
- mRNA 3'-end processing
Molecular Function
- DNA-binding transcription factor activity, RNA polymerase II-specific
- RNA binding
- mRNA binding
- protein binding
- metal ion binding
Cellular Component
- transcription export complex
- nucleoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000545588
- Coding exons
- 16
- Length
- 58471
- Individuals with no LoFs
- 125741
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 4
- Defined
- 125745
- p
- 0.0000159
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.69 | 335 | 434 | 0.772 | 0.0000233 | 5256 |
| Missense (PolyPhen) | 53 | 113.32 | 0.46769 | 1475 | ||
| Synonymous | 0.636 | 144 | 154 | 0.935 | 0.00000790 | 1601 |
| Loss of Function | 5.56 | 3 | 41.8 | 0.0718 | 0.00000240 | 516 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000036 | 0.000035 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Involved in nuclear mRNA export; probably mediated by association with the TREX complex. {ECO:0000269|PubMed:22928037}.;
Recessive Scores
- pRec
- 0.0851
Intolerance Scores
- RVIS EVS
- -0.33
- RVIS percentile EVS
- 30.74
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.994
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |