GATAD2B

GATA zinc finger domain containing 2B, the group of GATA zinc finger domain containing

Basic information

Region (hg38): 1:153789029-153923360

Links

ENSG00000143614 ∙ NCBI:57459 ∙ OMIM:614998 ∙ HGNC:30778 ∙ Uniprot:Q8WXI9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• 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

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
GAND syndrome (Mental retardation, autosomal dominant, 18)	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 ClinVar and linked to the GATAD2B gene.

• not provided (353 variants)
• Severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome (77 variants)
• Inborn genetic diseases (18 variants)
• not specified (16 variants)
• Intellectual disability (4 variants)
• See cases (3 variants)
• GATAD2B-Related Disorder (2 variants)
• GATAD2B-related intellectual disability syndrome (2 variants)
• GATAD2B-Related Neurodevelopmental Disorder (1 variants)
• Autism spectrum 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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			6	85	1	92
missense	1	3	136	7		147
nonsense	23	5	1			29
start loss						0
frameshift	25	4	1			30
inframe indel			1			1
splice donor/acceptor (+/-2bp)	6	2	1			9
splice region			9	4		13
non coding			2	43	30	75
Total	55	14	148	135	31

Highest pathogenic variant AF is 0.00000657

Variants in GATAD2B

This is a list of pathogenic ClinVar variants found in the GATAD2B region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-153796535-C-T			Likely benign (Apr 01, 2023)
1-153799559-G-A			Benign (Oct 01, 2022)
1-153799671-C-T			Likely benign (May 01, 2023)
1-153799672-G-A			Likely benign (Mar 01, 2023)
1-153799805-G-T			Likely benign (Jul 01, 2023)
1-153799871-G-T			Likely benign (May 01, 2023)
1-153799872-T-C			Likely benign (May 01, 2023)
1-153799990-G-A			Benign (Aug 01, 2022)
1-153800250-G-A			Likely benign (Jun 01, 2023)
1-153810179-A-G		Severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome	Likely pathogenic (Apr 18, 2019)
1-153810180-T-C			Uncertain significance (Jun 02, 2022)
1-153810192-G-A			Likely benign (Apr 09, 2023)
1-153810194-T-C			Uncertain significance (Jan 25, 2024)
1-153810196-G-C			Uncertain significance (Jan 17, 2024)
1-153810198-CT-C			Uncertain significance (Jun 01, 2018)
1-153810201-C-T			Likely benign (Jun 05, 2023)
1-153810202-G-A			Uncertain significance (Jul 25, 2023)
1-153810206-T-C		not specified • Severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome • Inborn genetic diseases	Conflicting classifications of pathogenicity (Dec 01, 2023)
1-153810211-C-T		not specified	Uncertain significance (Nov 13, 2015)
1-153810230-A-G			Likely benign (Nov 08, 2022)
1-153810248-G-A			Uncertain significance (Jul 18, 2023)
1-153810257-A-C			Uncertain significance (Aug 08, 2023)
1-153810257-A-G			Likely benign (Oct 05, 2023)
1-153810273-T-C			Uncertain significance (Dec 21, 2023)
1-153810278-C-T			Uncertain significance (Apr 22, 2023)

GnomAD

Source: gnomAD

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: dbNSFP

• 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

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