ZNF219
Basic information
Region (hg38): 14:21090077-21104722
Links
Phenotypes
GenCC
Source:
- microphthalmia (Limited), mode of inheritance: AR
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (98 variants)
- not_provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF219 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000016423.3. 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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | |||||
| missense | 96 | 98 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 97 | 3 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ZNF219 | protein_coding | protein_coding | ENST00000360947 | 4 | 14677 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.000228 | 119899 | 0 | 1 | 119900 | 0.00000417 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.92 | 271 | 444 | 0.610 | 0.0000321 | 4379 |
| Missense in Polyphen | 137 | 262.5 | 0.5219 | 2552 | ||
| Synonymous | 1.58 | 168 | 196 | 0.856 | 0.0000144 | 1601 |
| Loss of Function | 4.54 | 0 | 24.0 | 0.00 | 0.00000154 | 236 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000292 | 0.0000292 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcriptional regulator (PubMed:14621294, PubMed:19549071). Recognizes and binds 2 copies of the core DNA sequence motif 5'-GGGGG-3' (PubMed:14621294). Binds to the HMGN1 promoter and may repress HMGN1 expression (PubMed:14621294). Regulates SNCA expression in primary cortical neurons (PubMed:19549071). Binds to the COL2A1 promoter and activates COL2A1 expression, as part of a complex with SOX9 (By similarity). Plays a role in chondrocyte differentiation (By similarity). {ECO:0000250|UniProtKB:Q6IQX8, ECO:0000269|PubMed:14621294, ECO:0000269|PubMed:19549071}.;
- Pathway
- Ectoderm Differentiation
(Consensus)
Recessive Scores
- pRec
- 0.0946
Haploinsufficiency Scores
- pHI
- 0.312
- hipred
- Y
- hipred_score
- 0.572
- ghis
- 0.631
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.852
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Zfp219
- Phenotype
- homeostasis/metabolism phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- znf219
- Affected structure
- whole organism
- Phenotype tag
- abnormal
- Phenotype quality
- curved
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;regulation of neurotransmitter levels;transcription, DNA-templated;regulation of transcription, DNA-templated;G protein-coupled receptor signaling pathway;positive regulation of chondrocyte differentiation;negative regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;limb bud formation
- Cellular component
- nucleus;integral component of membrane
- Molecular function
- RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;histamine receptor activity;protein binding;metal ion binding