ZBTB20

zinc finger and BTB domain containing 20, the group of Zinc fingers C2H2-type|MicroRNA protein coding host genes|BTB domain containing

Basic information

Region (hg38): 3:114314499-115147292

Previous symbols: [ "ZNF288" ]

Links

ENSG00000181722 ∙ NCBI:26137 ∙ OMIM:606025 ∙ HGNC:13503 ∙ Uniprot:Q9HC78 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Primrose syndrome (Definitive), mode of inheritance: AD
• diabetes mellitus (Strong), mode of inheritance: AD
• Primrose syndrome (Strong), mode of inheritance: AD
• Primrose syndrome (Moderate), mode of inheritance: AD
• Primrose syndrome (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Primrose syndrome	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; Dermatologic; Musculoskeletal; Neurologic	25062845; 25017102; 27061120; 30256248

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZBTB20 gene.

• not provided (144 variants)
• Primrose syndrome (38 variants)
• Inborn genetic diseases (27 variants)
• not specified (8 variants)
• Intellectual disability (5 variants)
• Neurodevelopmental disorder (3 variants)
• Marfanoid habitus and intellectual disability (1 variants)
• ZBTB20-related condition (1 variants)
• - (1 variants)
• Autism spectrum disorder (1 variants)
• See cases (1 variants)
• Clinodactyly of the 5th finger;Autistic behavior;Moderate global developmental delay;Clinodactyly of the 4th toe;Abnormal facial shape (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZBTB20 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				43	4	47
missense	14	18	67	12	5	116
nonsense		2	3			5
start loss						0
frameshift	3	4	3			10
inframe indel			1			1
splice donor/acceptor (+/-2bp)		1	2			3
splice region			1			1
non coding			1	3	6	10
Total	17	25	77	58	15

Variants in ZBTB20

This is a list of pathogenic ClinVar variants found in the ZBTB20 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-114338999-T-C		not specified	Benign (Jul 17, 2020)
3-114339010-C-T		-	no classification for the single variant (-)
3-114339032-G-A		Primrose syndrome • ZBTB20-related disorder	Benign/Likely benign (Jan 22, 2024)
3-114339039-T-C			Uncertain significance (Mar 04, 2022)
3-114339049-C-T			Uncertain significance (May 03, 2023)
3-114339064-T-C			Uncertain significance (Mar 03, 2023)
3-114339076-C-T			Likely benign (Sep 01, 2022)
3-114339077-G-A			Likely benign (Oct 13, 2023)
3-114339077-G-C		ZBTB20-related disorder	Likely benign (Nov 08, 2022)
3-114339095-C-T			Likely benign (Apr 22, 2023)
3-114339102-G-A			Uncertain significance (Aug 14, 2023)
3-114339113-C-G			Likely benign (Jan 15, 2023)
3-114339115-C-T			Uncertain significance (Sep 27, 2023)
3-114339117-C-A		Primrose syndrome	Uncertain significance (Dec 11, 2023)
3-114339120-G-A			Uncertain significance (May 26, 2022)
3-114339132-C-G			Uncertain significance (Apr 14, 2022)
3-114339132-C-T			Uncertain significance (Jun 23, 2022)
3-114339133-G-A			Uncertain significance (Mar 01, 2022)
3-114339137-A-C			Likely benign (Oct 03, 2023)
3-114339141-G-A		Primrose syndrome • Inborn genetic diseases	Conflicting classifications of pathogenicity (Dec 20, 2023)
3-114339151-C-T			Likely benign (Oct 03, 2023)
3-114339153-G-A		not specified • ZBTB20-related disorder	Benign/Likely benign (Dec 18, 2023)
3-114339155-A-AG		Primrose syndrome	Uncertain significance (Mar 27, 2019)
3-114339158-G-A			Likely benign (Sep 03, 2023)
3-114339161-G-T			Benign/Likely benign (Jan 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZBTB20	protein_coding	protein_coding	ENST00000474710	4	809178

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.974	0.0262	125743	0	3	125746	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.27	217	481	0.452	0.0000335	4859
Missense in Polyphen		67	241.18	0.27781		2262
Synonymous	1.12	201	222	0.904	0.0000183	1493
Loss of Function	4.02	3	24.4	0.123	0.00000115	268

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000550	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.00000954	0.00000879
Middle Eastern	0.0000550	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be a transcription factor that may be involved in hematopoiesis, oncogenesis, and immune responses (PubMed:11352661). Plays a role in postnatal myogenesis, may be involved in the regulation of satellite cells self-renewal (By similarity). {ECO:0000250|UniProtKB:Q8K0L9, ECO:0000269|PubMed:11352661}.
• Disease: DISEASE: Primrose syndrome (PRIMS) [MIM:259050]: A disease characterized by macrocephaly, intellectual disability, disturbed behavior, dysmorphic facial features, ectopic calcifications, large calcified ear auricles, and progressive muscle wasting. {ECO:0000269|PubMed:25017102}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.151

Intolerance Scores

• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.49

Haploinsufficiency Scores

• pHI: 0.822
• hipred: Y
• hipred_score: 0.673

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.998

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zbtb20
• Phenotype: hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; vision/eye phenotype; muscle 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); growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;positive regulation of interferon-beta production;positive regulation of interleukin-6 production;positive regulation of tumor necrosis factor production;positive regulation of glycolytic process;positive regulation of lipid biosynthetic process;lipid homeostasis;cellular response to glucose stimulus
• Cellular component: nucleus;nucleoplasm;cytoplasm;nuclear body
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;transcription regulatory region DNA binding;metal ion binding