BEND3

BEN domain containing 3, the group of BEN domain containing

Basic information

Region (hg38): 6:107065182-107115515

Previous symbols: [ "KIAA1553" ]

Links

ENSG00000178409 ∙ NCBI:57673 ∙ OMIM:616374 ∙ HGNC:23040 ∙ Uniprot:Q5T5X7 ∙ 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 BEND3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BEND3 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					1	1
missense			35	2		37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	2	1

Variants in BEND3

This is a list of pathogenic ClinVar variants found in the BEND3 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-107068841-C-T		not specified	Uncertain significance (Sep 11, 2024)
6-107068871-G-T		not specified	Uncertain significance (Sep 03, 2024)
6-107069004-G-C		not specified	Uncertain significance (Nov 11, 2024)
6-107069207-C-T		not specified	Uncertain significance (Aug 12, 2024)
6-107069218-C-T		not specified	Uncertain significance (Mar 12, 2024)
6-107069227-T-C		not specified	Uncertain significance (Jan 26, 2023)
6-107069312-T-G		not specified	Uncertain significance (Jun 07, 2024)
6-107069360-T-A		not specified	Uncertain significance (Nov 18, 2022)
6-107069427-G-C		not specified	Uncertain significance (Apr 06, 2023)
6-107069472-G-T		not specified	Uncertain significance (Sep 29, 2023)
6-107069483-T-C		not specified	Uncertain significance (Dec 08, 2023)
6-107069533-C-G		not specified	Uncertain significance (Oct 07, 2024)
6-107069629-C-A		not specified	Uncertain significance (Oct 20, 2024)
6-107069707-C-T		not specified	Uncertain significance (Nov 16, 2021)
6-107069751-G-A			Benign (Mar 30, 2018)
6-107069768-G-A		not specified	Uncertain significance (Feb 15, 2023)
6-107069857-G-A		not specified	Uncertain significance (Jun 16, 2023)
6-107069915-G-A		not specified	Uncertain significance (Aug 13, 2021)
6-107069915-G-T		not specified	Uncertain significance (Apr 25, 2023)
6-107070095-C-T		not specified	Likely benign (Jul 25, 2023)
6-107070128-C-T		not specified	Uncertain significance (Jun 29, 2023)
6-107070136-C-A		not specified	Uncertain significance (Feb 06, 2024)
6-107070163-C-T		not specified	Uncertain significance (Aug 26, 2024)
6-107070212-C-T		not specified	Uncertain significance (Oct 01, 2024)
6-107070269-G-A		not specified	Uncertain significance (Jul 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BEND3	protein_coding	protein_coding	ENST00000429433	3	50088

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.936	0.0644	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.31	404	558	0.724	0.0000394	5443
Missense in Polyphen		155	263.53	0.58817		2370
Synonymous	-1.12	281	258	1.09	0.0000195	1666
Loss of Function	4.03	4	26.3	0.152	0.00000123	293

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000549	0.0000544
Finnish	0.0000928	0.0000924
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.0000549	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional repressor which associates with the NoRC (nucleolar remodeling complex) complex and plays a key role in repressing rDNA transcription. The sumoylated form modulates the stability of the NoRC complex component BAZ2A/TIP5 by controlling its USP21-mediated deubiquitination (PubMed:21914818, PubMed:26100909). Binds to unmethylated major satellite DNA and is involved in the recruitment of the Polycomb repressive complex 2 (PRC2) to major satellites (By similarity). Stimulates the ERCC6L translocase and ATPase activities (PubMed:28977671). {ECO:0000250|UniProtKB:Q6PAL0, ECO:0000269|PubMed:21914818, ECO:0000269|PubMed:26100909, ECO:0000269|PubMed:28977671}.

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.0480
• rvis_EVS: -1.06
• rvis_percentile_EVS: 7.54

Haploinsufficiency Scores

• pHI: 0.760
• hipred: Y
• hipred_score: 0.673
• ghis: 0.526

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.895

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bend3
• Phenotype: homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); pigmentation phenotype; hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;chromatin silencing at rDNA;DNA methylation;histone H4-K20 trimethylation;histone H3-K9 trimethylation;histone H4 acetylation;protein homooligomerization;histone H3-K4 trimethylation;histone H3-K27 trimethylation;positive regulation of ATP metabolic process
• Cellular component: nucleoplasm;nuclear heterochromatin;nucleolus
• Molecular function: rDNA binding;protein binding