GATAD2B
Basic information
Region (hg38): 1:153789030-153923360
Links
Phenotypes
GenCC
Source:
- severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome (Strong), mode of inheritance: AD
- severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome (Supportive), mode of inheritance: AD
- severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome (Strong), mode of inheritance: AD
- severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome (Definitive), mode of inheritance: AD
- severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome (Definitive), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
GAND syndrome | AD | Cardiovascular | The condition can involve congenital cardiac anomalies, and awareness may allow early management | Cardiovascular; Craniofacial; Musculoskeletal; Neurologic | 23033978; 31205050; 28077840; 30346093; 31205050; 31949314; 32688057 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (491 variants)
- Severe_intellectual_disability-poor_language-strabismus-grimacing_face-long_fingers_syndrome (108 variants)
- Inborn_genetic_diseases (51 variants)
- not_specified (19 variants)
- GATAD2B-related_disorder (12 variants)
- Intellectual_disability (4 variants)
- See_cases (4 variants)
- GATAD2B-related_intellectual_disability_syndrome (2 variants)
- Autism_spectrum_disorder (1 variants)
- GATAD2B-Related_Neurodevelopmental_Disorder (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the GATAD2B gene is commonly pathogenic or not. These statistics are base on transcript: NM_000020699.4. 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 | 125 | 132 | ||||
missense | 227 | 17 | 253 | |||
nonsense | 26 | 34 | ||||
start loss | 0 | |||||
frameshift | 36 | 12 | 50 | |||
splice donor/acceptor (+/-2bp) | 11 | 17 | ||||
Total | 78 | 25 | 239 | 142 | 2 |
Highest pathogenic variant AF is 0.00000371937
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
GATAD2B | protein_coding | protein_coding | ENST00000368655 | 10 | 118251 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.00 | 0.0000191 | 125744 | 0 | 2 | 125746 | 0.00000795 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 3.16 | 182 | 348 | 0.523 | 0.0000201 | 3862 |
Missense in Polyphen | 35 | 125.76 | 0.2783 | 1429 | ||
Synonymous | -0.124 | 126 | 124 | 1.01 | 0.00000639 | 1207 |
Loss of Function | 5.13 | 0 | 30.6 | 0.00 | 0.00000192 | 310 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000176 | 0.0000176 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcriptional repressor. Enhances MBD2-mediated repression. Efficient repression requires the presence of GATAD2A. Targets MBD3 to discrete loci in the nucleus. May play a role in synapse development. {ECO:0000269|PubMed:12183469, ECO:0000269|PubMed:16415179}.;
- Disease
- DISEASE: Mental retardation, autosomal dominant 18 (MRD18) [MIM:615074]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRD18 patients have severe intellectual disability and dysmorphic features. {ECO:0000269|PubMed:23033978, ECO:0000269|PubMed:23644463}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression;Positive epigenetic regulation of rRNA expression;Signal Transduction;Epigenetic regulation of gene expression;Gene expression (Transcription);Generic Transcription Pathway;HDACs deacetylate histones;RNA Polymerase I Promoter Clearance;RNA Polymerase II Transcription;Chromatin modifying enzymes;RNA Polymerase I Transcription;RNA Polymerase I Transcription Initiation;Regulation of PTEN gene transcription;PTEN Regulation;PIP3 activates AKT signaling;Chromatin organization;Regulation of TP53 Activity through Acetylation;Regulation of TP53 Activity;Transcriptional Regulation by TP53;Intracellular signaling by second messengers;Signaling events mediated by HDAC Class I
(Consensus)
Recessive Scores
- pRec
- 0.107
Intolerance Scores
- loftool
- 0.0548
- rvis_EVS
- -0.07
- rvis_percentile_EVS
- 48.54
Haploinsufficiency Scores
- pHI
- 0.765
- hipred
- Y
- hipred_score
- 0.794
- ghis
- 0.505
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.914
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Gatad2b
- Phenotype
Zebrafish Information Network
- Gene name
- gatad2b
- Affected structure
- smoothened signaling pathway
- Phenotype tag
- abnormal
- Phenotype quality
- increased process quality
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;ATP-dependent chromatin remodeling
- Cellular component
- nuclear chromatin;nucleoplasm;NuRD complex;nuclear speck;protein-containing complex
- Molecular function
- RNA polymerase II proximal promoter sequence-specific DNA binding;RNA polymerase II distal enhancer sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;protein binding;zinc ion binding;nucleosomal DNA binding