ZBTB18

zinc finger and BTB domain containing 18, the group of Zinc fingers C2H2-type|BTB domain containing

Basic information

Region (hg38): 1:244048547-244057476

Previous symbols: [ "ZNF238" ]

Links

ENSG00000179456 ∙ NCBI:10472 ∙ OMIM:608433 ∙ HGNC:13030 ∙ Uniprot:Q99592 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual disability, autosomal dominant 22 (Definitive), mode of inheritance: AD
• intellectual disability, autosomal dominant 22 (Strong), mode of inheritance: AD
• complex neurodevelopmental disorder (Definitive), mode of inheritance: AD
• intellectual disability, autosomal dominant 22 (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder, autosomal dominant 22	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Neurologic	24193349

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZBTB18 gene.

• not_provided (226 variants)
• Intellectual_disability,_autosomal_dominant_22 (72 variants)
• Inborn_genetic_diseases (53 variants)
• ZBTB18-related_disorder (16 variants)
• Intellectual_disability (6 variants)
• ZBTB18-related_intellectual_disability (2 variants)
• Marfanoid_habitus_and_intellectual_disability (1 variants)
• Renal_carnitine_transport_defect (1 variants)
• not_specified (1 variants)
• Neurodevelopmental_delay (1 variants)
• Neurodevelopmental_abnormality (1 variants)
• Developmental_delay (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZBTB18 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000205768.3. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	74	4	79
missense	3	30	134	16	11	194
nonsense	11	4	1			16
start loss						0
frameshift	18	10	2			30
splice donor/acceptor (+/-2bp)						0
Total	32	44	138	90	15

Highest pathogenic variant AF is 0.0000041046296

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZBTB18	protein_coding	protein_coding	ENST00000358704	2	6194

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00342	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.43	150	324	0.463	0.0000194	3542
Missense in Polyphen		27	127.87	0.21116		1382
Synonymous	-0.314	146	141	1.03	0.0000102	1012
Loss of Function	3.79	0	16.7	0.00	9.79e-7	203

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional repressor that plays a role in various developmental processes such as myogenesis and brain development. Plays a key role in myogenesis by directly repressing the expression of ID2 and ID3, 2 inhibitors of skeletal myogenesis. Also involved in controlling cell division of progenitor cells and regulating the survival of postmitotic cortical neurons. Specifically binds the consensus DNA sequence 5'- [AC]ACATCTG[GT][AC]-3' which contains the E box core, and acts by recruiting chromatin remodeling multiprotein complexes. May also play a role in the organization of chromosomes in the nucleus. {ECO:0000269|PubMed:9756912}.

Recessive Scores

• pRec: 0.121

Intolerance Scores

• rvis_EVS: -0.78
• rvis_percentile_EVS: 12.77

Haploinsufficiency Scores

• pHI: 0.959
• hipred: Y
• hipred_score: 0.728
• ghis: 0.633

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Zbtb18
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); 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); growth/size/body region phenotype; cellular phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;cellular response to DNA damage stimulus;skeletal muscle tissue development;negative regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II
• Cellular component: nuclear chromosome;nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;transcription coactivator activity;protein binding;sequence-specific DNA binding;metal ion binding