ADNP2
protein-codingADNP homeobox 2, the group of Zinc fingers C2H2-type|ZF class homeoboxes and pseudogenes
Gene summary
Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific. Predicted to be involved in nervous system development and regulation of gene expression. Predicted to be located in chromatin. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]
- ZNF508
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~38.3 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 ADNP2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_014913.4. 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 | 1 | 2 | 3 | |||
| missense | 164 | 17 | 181 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 166 | 19 | 0 | 185 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_055728.1 | 3 | MANE Select | |
| Ensembl | ENSP00000262198.3 | 3 | MANE Select | |
| Ensembl | ENSP00000453275.1 | 3 | Standard | |
| Ensembl | ENSP00000468397.1 | 3 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| adnp2a | Danio rerio | Structure: blood cell Quality: absent abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- regulation of transcription by RNA polymerase II
- neuron differentiation
- positive regulation of cell growth
- cellular response to oxidative stress
- negative regulation of cell death
Molecular Function
- DNA-binding transcription factor activity, RNA polymerase II-specific
- molecular_function
- DNA binding
- protein binding
- metal ion binding
Cellular Component
- cellular_component
- nucleus
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000262198
- Coding exons
- 3
- Length
- 38492
- Individuals with no LoFs
- 125727
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 21
- Defined
- 125748
- p
- 0.0000835
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.340 | 596 | 620 | 0.962 | 0.0000332 | 7347 |
| Missense (PolyPhen) | 164 | 199.34 | 0.8227 | 2593 | ||
| Synonymous | -2.14 | 297 | 254 | 1.17 | 0.0000153 | 2384 |
| Loss of Function | 4.08 | 6 | 30.2 | 0.199 | 0.00000160 | 402 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0.00012 | 0.00012 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.000089 | 0.000088 | rare |
| South Asian | 0.00013 | 0.00013 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May be involved in transcriptional regulation.;
Recessive Scores
- pRec
- 0.106
Intolerance Scores
- LoFtool
- 0.0420
- RVIS EVS
- -1.5
- RVIS percentile EVS
- 3.6
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.897
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |