UNK

protein-coding

unk 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]

Previous symbols:
  • ZC3HDC5
  • ZC3H5

MANE transcript

NM_001080419.3

Inheritance

AR

ClinVar variants

U:81B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.07

Max pathogenic AF

—

Genomic locus

chr17:75,784,806-75,825,799

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~41.0 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

complex neurodevelopmental disorderLIMITED

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

2 Conditions Cataloged
not specifiedTotal: 74
not providedTotal: 3

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.

EffectPLPVUSLBBSum
synonymous
3
clinvar
1
clinvar
4
missense
73
clinvar
2
clinvar
75
nonsense
1
clinvar
1
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
4
clinvar
4
Total00812184
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 33 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001080419.3RefSeqNP_001073888.216MANE Select
ENST00000589666.6EnsemblENSP00000464893.116MANE Select
ENST00000586217.1EnsemblENSP00000466054.11Standard
ENST00000586527.1EnsemblENSP00000467849.12Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense3.722614940.5290.00003105214
Missense (PolyPhen)87230.620.377252301
Synonymous1.601882180.8620.00001551606
Loss of Function5.49340.80.07350.00000212459

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American0.0000290.000029rare
Ashkenazi Jewish0.000100.000099rare
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)0.0000360.000035rare
South Asian0.0000340.000033rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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