ZBED6

zinc finger BED-type containing 6, the group of DNA transposon derived genes|Zinc fingers BED-type

Basic information

Region (hg38): 1:203795622-203854124

Links

ENSG00000257315 ∙ NCBI:100381270 ∙ OMIM:613512 ∙ HGNC:33273 ∙ Uniprot:P86452 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZBED6 gene.

• Inborn genetic diseases (67 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZBED6 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						0
missense			34	3		37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding			27	2	1	30
Total	0	0	61	5	1

Variants in ZBED6

This is a list of pathogenic ClinVar variants found in the ZBED6 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-203797619-A-G		not specified	Uncertain significance (Mar 07, 2023)
1-203797623-A-T		not specified	Uncertain significance (Feb 10, 2023)
1-203797721-G-A		not specified	Uncertain significance (May 31, 2023)
1-203797746-G-A		not specified	Uncertain significance (May 30, 2023)
1-203797791-G-A		not specified	Uncertain significance (Dec 19, 2023)
1-203797803-C-T		not specified	Uncertain significance (Jan 20, 2023)
1-203797823-T-G		not specified	Uncertain significance (Jan 03, 2024)
1-203797998-G-A		not specified	Uncertain significance (Jul 06, 2021)
1-203798157-A-T		not specified	Uncertain significance (Feb 06, 2023)
1-203798237-G-A		not specified	Uncertain significance (Mar 11, 2022)
1-203798246-G-C		not specified	Uncertain significance (Jan 05, 2022)
1-203798247-C-T		not specified	Uncertain significance (Sep 16, 2021)
1-203798292-C-T		not specified	Uncertain significance (Jun 06, 2023)
1-203798519-G-C		not specified	Uncertain significance (Sep 14, 2022)
1-203798540-A-C		not specified	Uncertain significance (May 31, 2023)
1-203798546-C-T		not specified	Uncertain significance (Aug 16, 2022)
1-203798579-A-C		not specified	Uncertain significance (Jun 17, 2022)
1-203798607-A-T		not specified	Uncertain significance (Jul 14, 2021)
1-203798675-G-A		not specified	Uncertain significance (Nov 08, 2022)
1-203798697-T-C		not specified	Uncertain significance (Aug 12, 2021)
1-203798705-C-G		not specified	Uncertain significance (Dec 13, 2022)
1-203798787-T-C		not specified	Uncertain significance (Feb 21, 2024)
1-203798792-C-T		not specified	Uncertain significance (Mar 14, 2023)
1-203798799-A-G		not specified	Uncertain significance (Jan 02, 2024)
1-203798808-C-T		not specified	Uncertain significance (Feb 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZBED6	protein_coding	protein_coding	ENST00000550078	1	4250

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000399	0.999	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.28	347	489	0.709	0.0000232	6493
Missense in Polyphen		100	194.44	0.5143		2615
Synonymous	0.657	166	177	0.937	0.00000887	1859
Loss of Function	3.11	11	29.1	0.378	0.00000156	393

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 which binds to the consensus sequence 5'-GCTCGC-3' and represses transcription of IGF2. May also regulate expression of other target genes containing this consensus binding site (By similarity). {ECO:0000250}.

Haploinsufficiency Scores

• ghis: 0.412

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zbed6
• Phenotype: muscle phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype; renal/urinary system phenotype; liver/biliary system phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;negative regulation of transcription, DNA-templated
• Cellular component: nucleus;nucleolus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;metal ion binding;protein dimerization activity