ZNF516
protein-codingzinc finger protein 516, the group of Zinc fingers C2H2-type
Gene summary
Zinc-finger proteins bind nucleic acids and play important roles in various cellular functions, including cell proliferation, differentiation, and apoptosis. This gene encodes a zinc-finger protein, and belongs to the krueppel C2H2-type zinc-finger protein family. It may be involved in transcriptional regulation. [provided by RefSeq, Sep 2012]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~137.6 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 ZNF516 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_014643.4. 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 | 2 | 3 | 8 | ||
| missense | 214 | 15 | 229 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 219 | 17 | 3 | 239 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_055458.1 | 5 | MANE Select | |
| Ensembl | ENSP00000394757.2 | 5 | MANE Select | |
| Ensembl | ENSP00000446211.1 | 1 | Standard | |
| Ensembl | ENSP00000445902.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Thermogenesis - Homo sapiens (human)
Biological Process
- regulation of transcription by RNA polymerase II
- response to cold
- positive regulation of transcription, DNA-templated
- brown fat cell differentiation
- adipose tissue development
Molecular Function
- DNA-binding transcription factor activity, RNA polymerase II-specific
- proximal promoter sequence-specific DNA binding
- activating transcription factor binding
- metal ion binding
Cellular Component
- nucleus
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000443185
- Coding exons
- 6
- Length
- 137503
- Individuals with no LoFs
- 2645
- Homozygous LoFs
- 121702
- Heterozygous LoFs
- 297
- Defined
- 124644
- p
- 0.854
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.992 | 720 | 799 | 0.901 | 0.0000576 | 7466 |
| Missense (PolyPhen) | 141 | 255.92 | 0.55095 | 2348 | ||
| Synonymous | -2.41 | 431 | 372 | 1.16 | 0.0000316 | 2385 |
| Loss of Function | 5.23 | 2 | 35.7 | 0.0559 | 0.00000176 | 387 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 1.0 | 0.78 | notable |
| Latino/Admixed American | 1.0 | 0.92 | notable |
| Ashkenazi Jewish | 1.0 | 0.88 | notable |
| East Asian | 1.0 | 0.91 | notable |
| Finnish | 1.0 | 0.80 | notable |
| European (Non-Finnish) | 1.0 | 0.84 | notable |
| South Asian | 1.0 | 0.94 | notable |
| Other | 1.0 | 0.88 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Transcriptional regulator that binds to the promoter and activates the transcription of genes promoting brown adipose tissue (BAT) differentiation. Among brown adipose tissue-specific genes, binds the proximal region of the promoter of the UCP1 gene to activate its transcription and thereby regulate thermogenesis (By similarity). May also play a role in the cellular response to replication stress (PubMed:23446422). {ECO:0000250|UniProtKB:Q7TSH3, ECO:0000269|PubMed:23446422}.;
Recessive Scores
- pRec
- 0.105
Essentials
- Essential (CRISPR2)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.737
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |