ZBED1

zinc finger BED-type containing 1, the group of Zinc fingers BED-type|Pseudoautosomal region 1

Basic information

Region (hg38): X:2486413-2500976

Previous symbols: [ "ALTE" ]

Links

ENSG00000214717 ∙ NCBI:9189 ∙ OMIM:300178 ∙ HGNC:447 ∙ Uniprot:O96006 ∙ 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 ZBED1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZBED1 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					12	12
missense					4	4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	0	16

Variants in ZBED1

This is a list of pathogenic ClinVar variants found in the ZBED1 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-2488738-T-G			Benign (Mar 29, 2018)
X-2488954-T-C			Benign (Mar 29, 2018)
X-2489148-G-A			Benign (Dec 11, 2017)
X-2489805-G-T			Benign (Feb 08, 2018)
X-2489886-C-T			Benign (May 30, 2018)
X-2490504-G-A			Benign (May 30, 2018)
X-2490552-G-A			Benign (Mar 29, 2018)
X-2490618-G-A			Benign (Mar 29, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZBED1	protein_coding	protein_coding	ENST00000381223	1	14554

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000362	0.990	125557	0	34	125591	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.847	404	455	0.888	0.0000344	4564
Missense in Polyphen		99	139.71	0.70861		1504
Synonymous	-0.999	245	226	1.08	0.0000200	1410
Loss of Function	2.29	9	20.1	0.448	9.76e-7	221

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000296	0.000296
Ashkenazi Jewish	0.000102	0.0000992
East Asian	0.000163	0.000163
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000133	0.000123
Middle Eastern	0.000163	0.000163
South Asian	0.0000653	0.0000653
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to 5'-TGTCG[CT]GA[CT]A-3' DNA elements found in the promoter regions of a number of genes related to cell proliferation. Binds to the histone H1 promoter and stimulates transcription. Was first identified as gene weakly similar to Ac transposable elements, but does not code for any transposase activity. {ECO:0000269|PubMed:12663651}.
• Pathway: SUMOylation of chromatin organization proteins;Post-translational protein modification;SUMO E3 ligases SUMOylate target proteins;Metabolism of proteins;SUMOylation (Consensus)

Recessive Scores

• pRec: 0.163

Intolerance Scores

• loftool: 0.142
• rvis_EVS: -2.19
• rvis_percentile_EVS: 1.39

Haploinsufficiency Scores

• pHI: 0.101
• hipred: N
• hipred_score: 0.374
• ghis: 0.515

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.972

Gene Damage Prediction

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

Gene ontology

• Biological process: protein sumoylation;positive regulation of transcription by RNA polymerase II
• Cellular component: nuclear chromosome;nucleoplasm
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;protein binding;SUMO transferase activity;identical protein binding;sequence-specific DNA binding;metal ion binding;protein dimerization activity