BEND6

BEN domain containing 6, the group of BEN domain containing

Basic information

Region (hg38): 6:56955107-57027346

Previous symbols: [ "C6orf65" ]

Links

ENSG00000151917 ∙ NCBI:221336 ∙ ∙ HGNC:20871 ∙ Uniprot:Q5SZJ8 ∙ 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 BEND6 gene.

• not_specified (25 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BEND6 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000152731.3. 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						0
missense			24	1		25
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	24	1	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BEND6	protein_coding	protein_coding	ENST00000370746	5	72368

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000769	0.933	124779	0	14	124793	0.0000561

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.712	114	137	0.829	0.00000669	1836
Missense in Polyphen		40	47.918	0.83475		701
Synonymous	0.555	46	51.0	0.901	0.00000268	502
Loss of Function	1.63	7	13.4	0.521	7.18e-7	167

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000735	0.0000735
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000556
Finnish	0.0000929	0.0000928
European (Non-Finnish)	0.0000442	0.0000441
Middle Eastern	0.0000556	0.0000556
South Asian	0.0000710	0.0000654
Other	0.000342	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a corepressor of recombining binding protein suppressor hairless (RBPJ) and inhibits Notch signaling in neural stem cells, thereby opposing their self-renewal and promoting neurogenesis (PubMed:23571214). {ECO:0000269|PubMed:23571214}.

Intolerance Scores

• loftool: 0.411
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.07

Haploinsufficiency Scores

• pHI: 0.245
• hipred: N
• hipred_score: 0.292
• ghis: 0.638

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.214

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bend6

Gene ontology

• Biological process: positive regulation of neuron differentiation;negative regulation of Notch signaling pathway;negative regulation of nucleic acid-templated transcription
• Cellular component: nucleus
• Molecular function: chromatin binding;transcription corepressor activity