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): 3:114314500-115147292

Previous symbols: [ "ZNF288" ]

Links

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

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 365.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_001348800.3	NP_001335729.1	4	yes	-
ENST00000675478.1	ENSP00000501561.1	4	yes	-
NM_015642.7	NP_056457.3	2	-	-
NM_001164342.2	NP_001157814.1	4	-	-

Phenotypes

GenCC

Source: genCC

• Primrose syndrome (Moderate), mode of inheritance: AD
• Primrose syndrome (Definitive), mode of inheritance: AD
• diabetes mellitus (Strong), mode of inheritance: AD
• Primrose syndrome (Strong), mode of inheritance: AD
• Primrose syndrome (Strong), mode of inheritance: AD
• Primrose syndrome (Definitive), 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 (338 variants)
• Primrose_syndrome (75 variants)
• Inborn_genetic_diseases (62 variants)
• ZBTB20-related_disorder (28 variants)
• not_specified (13 variants)
• Intellectual_disability (7 variants)
• Neurodevelopmental_disorder (3 variants)
• Moderate_global_developmental_delay (1 variants)
• Autism_spectrum_disorder (1 variants)
• SHORT_syndrome (1 variants)
• Clinodactyly_of_the_4th_toe (1 variants)
• See_cases (1 variants)
• Marfanoid_habitus_and_intellectual_disability (1 variants)
• Abnormal_facial_shape (1 variants)
• Clinodactyly_of_the_5th_finger (1 variants)
• Autistic_behavior (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. These statistics are base on transcript: NM_001348800.3. 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	110	4	115
missense	28	34	157	40	14	273
nonsense	3	4	3	1		11
start loss						0
frameshift	10	9	2			21
splice donor/acceptor (+/-2bp)	1	2	2			5
Total	42	49	165	151	18

Highest pathogenic variant AF is 0.000010533843

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
		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

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

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