UNK
protein-codingunk zinc finger, the group of Zinc fingers CCCH-type
Gene summary
Enables mRNA CDS binding activity. Involved in cell morphogenesis involved in neuron differentiation and negative regulation of cytoplasmic translation. Located in cytosol. [provided by Alliance of Genome Resources, Jun 2026]
- ZC3HDC5
- ZC3H5
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~41.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0100038
Submitter: LiferaOmics
Genetic evidence – Published (AR scope) No scorable published cases of biallelic (autosomal recessive) UNK variants causing a defined neurodevelopmental disorder were identified in the literature. Published genetic evidence total = 0 / 12 Published (AD context; not scored for AR) PMID: 33057194 – Large-scale developmental disorder sequencing study identifying genes enriched for de novo (monoallelic) variants in neurodevelopmental phenotypes. This represents a dominant/de novo context and is not scorable under the autosomal recessive model. PMID: 31785789 – Cohort-based neurodevelopmental disorder sequencing study focused on de novo enrichment analyses. No biallelic AR UNK cases reported. Not scorable for AR. ClinGen Gene–Disease Validity curation – No autosomal recessive neurodevelopmental disorder has been curated for UNK. No AR classification exists. AD-context evidence total (not scored for AR) = 0 Genetic evidence – Our case Family 1 – One proband. Case-level (biallelic predicted null in AR model; homozygous frameshift; consanguinity −0.5 applied) = 1.5; Consanguinity deduction = −0.5; Case-level score = 1.0; Segregation = 0; Case-control = 0 Family 1 total = 1.0 Total genetic evidence (published AR + our case) 1.0 / 12 Experimental evidence – Published (conservative and phenotype-aligned) No experimental evidence was scored at this time. Although UNK has reported roles in neuronal development in model systems, there is currently no experimental evidence directly modeling or functionally validating an autosomal recessive UNK-related neurodevelopmental disorder with phenotype alignment sufficient for scoring under ClinGen criteria. Experimental evidence total = 0 / 6 Overall score Genetic evidence = 1.0 Experimental evidence = 0 Total = 1.0
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to UNK variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001080419.3. 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 | 3 | 1 | 4 | |||
| missense | 73 | 2 | 75 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 81 | 2 | 1 | 84 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001073888.2 | 16 | MANE Select | |
| Ensembl | ENSP00000464893.1 | 16 | MANE Select | |
| Ensembl | ENSP00000466054.1 | 1 | Standard | |
| Ensembl | ENSP00000467849.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- neuron migration
- cell morphogenesis involved in neuron differentiation
- negative regulation of cytoplasmic translation
Molecular Function
- RNA binding
- metal ion binding
- polysome binding
- mRNA CDS binding
Cellular Component
- cytoplasm
- polysome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000589666
- Coding exons
- 16
- Length
- 41206
- Individuals with no LoFs
- 124790
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 7
- Defined
- 124797
- p
- 0.0000280
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 3.72 | 261 | 494 | 0.529 | 0.0000310 | 5214 |
| Missense (PolyPhen) | 87 | 230.62 | 0.37725 | 2301 | ||
| Synonymous | 1.60 | 188 | 218 | 0.862 | 0.0000155 | 1606 |
| Loss of Function | 5.49 | 3 | 40.8 | 0.0735 | 0.00000212 | 459 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000036 | 0.000035 | rare |
| South Asian | 0.000034 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Sequence-specific RNA-binding protein which plays an important role in the establishment and maintenance of the early morphology of cortical neurons during embryonic development. Acts as a translation repressor and controls a translationally regulated cell morphology program to ensure proper structuring of the nervous system. Translational control depends on recognition of its binding element within target mRNAs which consists of a mandatory UAG trimer upstream of a U/A-rich motif. Associated with polysomes (PubMed:25737280). {ECO:0000269|PubMed:25737280}.;
Recessive Scores
- pRec
- 0.206
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.951
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |