ZBED5

zinc finger BED-type containing 5, the group of Zinc fingers BED-type

Basic information

Region (hg38): 11:10812074-10858796

Links

ENSG00000236287 ∙ NCBI:58486 ∙ OMIM:615251 ∙ HGNC:30803 ∙ Uniprot:Q49AG3 ∙ 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 ZBED5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZBED5 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				2		2
missense			31			31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	2	0

Variants in ZBED5

This is a list of pathogenic ClinVar variants found in the ZBED5 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-10852961-A-C		not specified	Uncertain significance (Aug 14, 2023)
11-10852971-T-C		not specified	Uncertain significance (May 04, 2022)
11-10852973-T-C		not specified	Uncertain significance (Jan 23, 2024)
11-10853009-G-A		not specified	Uncertain significance (Nov 27, 2023)
11-10853021-T-C		not specified	Uncertain significance (Nov 29, 2023)
11-10853043-G-A		not specified	Uncertain significance (Feb 23, 2023)
11-10853051-A-G		not specified	Uncertain significance (May 12, 2024)
11-10853177-C-T		not specified	Uncertain significance (Feb 11, 2022)
11-10853237-T-C		not specified	Uncertain significance (Nov 13, 2023)
11-10853238-T-C		not specified	Uncertain significance (Mar 29, 2022)
11-10853276-C-T		not specified	Uncertain significance (Feb 28, 2023)
11-10853277-G-A		not specified	Uncertain significance (May 06, 2024)
11-10853330-G-A		not specified	Uncertain significance (Apr 17, 2023)
11-10853338-T-A		not specified	Uncertain significance (Oct 25, 2023)
11-10853342-G-C		not specified	Uncertain significance (Nov 07, 2022)
11-10853384-T-A		not specified	Uncertain significance (Jul 05, 2023)
11-10853426-G-A		not specified	Uncertain significance (Jul 14, 2021)
11-10853430-A-T		not specified	Uncertain significance (Mar 11, 2024)
11-10853473-C-T		not specified	Uncertain significance (Feb 16, 2023)
11-10853938-T-C			Likely benign (Dec 01, 2022)
11-10854267-T-C		not specified	Uncertain significance (Apr 14, 2023)
11-10854343-A-C		not specified	Uncertain significance (Dec 21, 2022)
11-10854350-T-C		not specified	Uncertain significance (Nov 17, 2023)
11-10854353-T-C		not specified	Uncertain significance (Mar 01, 2023)
11-10854408-G-T		not specified	Uncertain significance (Oct 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZBED5	protein_coding	protein_coding	ENST00000432999	1	46723

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.713	0.287	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.87	259	359	0.722	0.0000184	4555
Missense in Polyphen		39	73.431	0.53111		1013
Synonymous	2.50	94	130	0.721	0.00000653	1345
Loss of Function	3.51	4	21.6	0.185	0.00000127	292

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

Haploinsufficiency Scores

• ghis: 0.431

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.466

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zbed5

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II
• Cellular component: nucleoplasm
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;metal ion binding