BEND7

BEN domain containing 7, the group of BEN domain containing

Basic information

Region (hg38): 10:13438484-13529014

Previous symbols: [ "C10orf30" ]

Links

ENSG00000165626 ∙ NCBI:222389 ∙ ∙ HGNC:23514 ∙ Uniprot:Q8N7W2 ∙ 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 BEND7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BEND7 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			32	1		33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	1	0

Variants in BEND7

This is a list of pathogenic ClinVar variants found in the BEND7 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-13439183-G-T		not specified	Uncertain significance (Sep 03, 2024)
10-13439194-T-G		not specified	Uncertain significance (Jan 23, 2024)
10-13439233-T-C		not specified	Uncertain significance (Aug 19, 2024)
10-13439252-G-A		not specified	Uncertain significance (Aug 04, 2023)
10-13439291-G-T		not specified	Uncertain significance (Apr 16, 2024)
10-13439369-G-A		not specified	Uncertain significance (Jul 14, 2021)
10-13439395-A-G		not specified	Uncertain significance (Mar 28, 2024)
10-13439422-T-A		not specified	Uncertain significance (Jul 14, 2024)
10-13439431-C-T		not specified	Likely benign (Jun 29, 2022)
10-13439470-A-C		not specified	Uncertain significance (Jan 07, 2025)
10-13439471-G-T		not specified	Uncertain significance (Jan 17, 2023)
10-13439477-T-C		not specified	Uncertain significance (May 17, 2023)
10-13447310-G-A		not specified	Uncertain significance (Aug 16, 2021)
10-13447314-T-A		not specified	Uncertain significance (Apr 08, 2024)
10-13452637-G-T		not specified	Uncertain significance (Feb 22, 2023)
10-13452653-T-C		not specified	Uncertain significance (Aug 10, 2024)
10-13480946-T-C		not specified	Uncertain significance (Dec 14, 2022)
10-13480954-T-G		not specified	Uncertain significance (Apr 18, 2023)
10-13480997-T-G		not specified	Uncertain significance (Apr 23, 2024)
10-13481006-A-C		not specified	Uncertain significance (Aug 28, 2024)
10-13481012-C-G		not specified	Uncertain significance (Jan 23, 2023)
10-13481018-A-C		not specified	Uncertain significance (Apr 01, 2024)
10-13481046-G-A		not specified	Uncertain significance (Feb 23, 2023)
10-13481052-A-G		not specified	Uncertain significance (Feb 15, 2023)
10-13481066-G-A		not specified	Uncertain significance (Oct 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BEND7	protein_coding	protein_coding	ENST00000341083	7	90491

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00607	0.990	125740	0	7	125747	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.648	232	262	0.887	0.0000144	3006
Missense in Polyphen		70	102.01	0.68619		1215
Synonymous	-0.931	115	103	1.12	0.00000608	954
Loss of Function	2.52	7	18.8	0.372	9.63e-7	223

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000600	0.0000600
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000266	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.806
• rvis_EVS: -0.33
• rvis_percentile_EVS: 30.7

Haploinsufficiency Scores

• pHI: 0.115
• hipred: N
• hipred_score: 0.380
• ghis: 0.541

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.517

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bend7

Gene ontology

• Cellular component: extracellular exosome
• Molecular function: protein binding