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

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 20.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_001367314.1	NP_001354243.1	3	yes	-
ENST00000369042.6	ENSP00000358038.1	3	yes	-
NM_001080450.3	NP_001073919.1	3	-	-
ENST00000429433.3	ENSP00000411268.2	3	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BEND3 gene.

• not_specified (108 variants)
• not_provided (1 variants)

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. These statistics are base on transcript: NM_001367314.1. 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				1	1	2
missense			102	5		107
nonsense			2			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	104	6	1

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
		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

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

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