ZBED2

zinc finger BED-type containing 2, the group of Zinc fingers BED-type

Basic information

Region (hg38): 3:111592900-111595346

Links

ENSG00000177494 ∙ NCBI:79413 ∙ OMIM:615246 ∙ HGNC:20710 ∙ Uniprot:Q9BTP6 ∙ 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 ZBED2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZBED2 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in ZBED2

This is a list of pathogenic ClinVar variants found in the ZBED2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-111593612-G-A		not specified	Uncertain significance (May 23, 2023)
3-111593689-C-G		not specified	Uncertain significance (Jun 22, 2023)
3-111593693-C-A		not specified	Uncertain significance (Feb 17, 2024)
3-111593721-G-T		not specified	Uncertain significance (Jun 03, 2022)
3-111593790-T-A		not specified	Uncertain significance (Apr 23, 2024)
3-111593793-C-T		not specified	Uncertain significance (Mar 03, 2022)
3-111593820-C-T		not specified	Uncertain significance (Mar 15, 2024)
3-111593840-C-T		not specified	Uncertain significance (May 04, 2022)
3-111593841-G-C		not specified	Uncertain significance (Oct 21, 2021)
3-111593849-G-T		not specified	Uncertain significance (Aug 02, 2021)
3-111593993-T-C		not specified	Uncertain significance (Feb 22, 2023)
3-111594045-G-A		not specified	Uncertain significance (Feb 13, 2024)
3-111594078-T-A		not specified	Uncertain significance (Dec 26, 2023)
3-111594078-T-C		not specified	Uncertain significance (Jun 16, 2023)
3-111594092-G-C		not specified	Uncertain significance (Mar 06, 2023)
3-111594108-C-T		not specified	Uncertain significance (Apr 29, 2024)
3-111594161-A-G		not specified	Uncertain significance (Sep 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZBED2	protein_coding	protein_coding	ENST00000317012	1	2544

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000445	0.438	125731	0	13	125744	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0986	134	131	1.02	0.00000723	1437
Missense in Polyphen		22	25.724	0.85522		310
Synonymous	-0.112	47	46.0	1.02	0.00000229	423
Loss of Function	0.0703	5	5.17	0.967	2.21e-7	61

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.00	0.00
Finnish	0.0000993	0.0000924
European (Non-Finnish)	0.0000629	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.264
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.37

Haploinsufficiency Scores

• pHI: 0.0533
• hipred: N
• hipred_score: 0.146
• ghis: 0.485

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.528

Gene Damage Prediction

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

Gene ontology

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