BEND5

BEN domain containing 5, the group of BEN domain containing

Basic information

Region (hg38): 1:48727518-48776969

Previous symbols: [ "C1orf165" ]

Links

ENSG00000162373 ∙ NCBI:79656 ∙ ∙ HGNC:25668 ∙ Uniprot:Q7L4P6 ∙ 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 BEND5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BEND5 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			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	2	0

Variants in BEND5

This is a list of pathogenic ClinVar variants found in the BEND5 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-48727938-T-C		not specified	Uncertain significance (Jul 11, 2022)
1-48727942-T-C		Malignant tumor of prostate	Uncertain significance (-)
1-48736312-G-A			Likely benign (Mar 01, 2023)
1-48742660-G-A		not specified	Uncertain significance (Feb 06, 2023)
1-48742706-T-C		not specified	Uncertain significance (Feb 06, 2023)
1-48742724-C-T		not specified	Uncertain significance (Dec 20, 2021)
1-48758956-T-A		not specified	Uncertain significance (Dec 09, 2023)
1-48758957-C-T		not specified	Uncertain significance (Dec 09, 2023)
1-48759028-C-T		not specified	Uncertain significance (Dec 27, 2022)
1-48759053-G-A		not specified	Uncertain significance (May 31, 2024)
1-48759071-G-T		not specified	Uncertain significance (Dec 14, 2021)
1-48759131-T-C		not specified	Uncertain significance (Apr 26, 2024)
1-48759137-T-C		not specified	Uncertain significance (Aug 13, 2021)
1-48759164-C-A		not specified	Uncertain significance (Feb 16, 2023)
1-48759164-C-T		not specified	Uncertain significance (May 01, 2022)
1-48759178-G-A		not specified	Uncertain significance (May 31, 2022)
1-48759190-T-C		not specified	Uncertain significance (May 30, 2023)
1-48759265-G-T		not specified	Uncertain significance (Jan 31, 2022)
1-48761340-G-C		not specified	Uncertain significance (May 27, 2022)
1-48761376-T-G		not specified	Uncertain significance (Sep 14, 2023)
1-48776645-C-A		not specified	Uncertain significance (Mar 03, 2022)
1-48776699-C-T		not specified	Uncertain significance (May 28, 2024)
1-48776784-C-T			Likely benign (Jul 01, 2022)
1-48776807-C-T		not specified	Uncertain significance (Dec 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BEND5	protein_coding	protein_coding	ENST00000371833	6	49447

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0543	0.942	125737	0	10	125747	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.70	152	224	0.679	0.0000134	2735
Missense in Polyphen		51	81.379	0.6267		984
Synonymous	-0.538	100	93.4	1.07	0.00000606	806
Loss of Function	2.54	5	16.0	0.313	6.80e-7	226

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.000114	0.0000992
East Asian	0.0000553	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000536	0.0000527
Middle Eastern	0.0000553	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a transcriptional repressor (PubMed:23468431). {ECO:0000269|PubMed:23468431}.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.241
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.32

Haploinsufficiency Scores

• pHI: 0.626
• hipred: Y
• hipred_score: 0.593
• ghis: 0.539

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.791

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bend5

Gene ontology

• Biological process: negative regulation of transcription, DNA-templated
• Cellular component: Golgi apparatus
• Molecular function: DNA binding;protein binding