BANP

BTG3 associated nuclear protein, the group of BEN domain containing

Basic information

Region (hg38): 16:87949244-88077318

Links

ENSG00000172530 ∙ NCBI:54971 ∙ OMIM:611564 ∙ HGNC:13450 ∙ Uniprot:Q8N9N5 ∙ 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 BANP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BANP 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	2
missense			36			36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	1	1

Variants in BANP

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

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

Position	Type	Phenotype	Significance	ClinVar
16-87975123-C-T		not specified	Uncertain significance (Nov 25, 2024)
16-87975176-G-A		not specified	Uncertain significance (Mar 29, 2023)
16-87981071-G-A		not specified	Uncertain significance (Dec 28, 2022)
16-87981093-G-A		not specified	Uncertain significance (Aug 05, 2024)
16-87984084-A-G		not specified	Uncertain significance (Dec 09, 2024)
16-87984125-A-T		not specified	Uncertain significance (Jul 15, 2021)
16-87984175-C-T		not specified	Uncertain significance (Apr 04, 2024)
16-87984190-G-A		not specified	Uncertain significance (Dec 01, 2022)
16-87984207-A-T		not specified	Uncertain significance (Jan 01, 2025)
16-87984237-C-G		not specified	Uncertain significance (Jan 04, 2024)
16-88004354-A-T		not specified	Uncertain significance (Dec 25, 2024)
16-88004376-C-G		not specified	Uncertain significance (Dec 27, 2022)
16-88006091-G-T		not specified	Uncertain significance (Dec 23, 2024)
16-88006104-G-A		not specified	Uncertain significance (Jan 10, 2023)
16-88006107-G-A		not specified	Uncertain significance (May 23, 2023)
16-88006119-T-C		not specified	Uncertain significance (Nov 21, 2023)
16-88006172-G-A		not specified	Uncertain significance (Oct 19, 2024)
16-88006217-A-G		not specified	Uncertain significance (Mar 25, 2024)
16-88006228-C-T			Likely benign (Apr 01, 2022)
16-88018464-A-G		Ependymoma	Uncertain significance (Dec 29, 2017)
16-88027562-G-A			Benign (Jul 05, 2018)
16-88027597-C-T		not specified	Uncertain significance (Dec 21, 2022)
16-88027645-C-T		not specified	Uncertain significance (Aug 19, 2024)
16-88033109-A-C		not specified	Uncertain significance (Nov 25, 2024)
16-88033121-G-T		not specified	Uncertain significance (Jul 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BANP	protein_coding	protein_coding	ENST00000393207	13	128075

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.994	0.00612	125742	0	5	125747	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.43	219	346	0.633	0.0000238	3370
Missense in Polyphen		107	218.25	0.49026		2107
Synonymous	-1.49	181	157	1.15	0.0000129	1000
Loss of Function	4.42	3	28.4	0.106	0.00000139	291

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000905	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000672	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Controls V(D)J recombination during T-cell development by repressing T-cell receptor (TCR) beta enhancer function. Binds to scaffold/matrix attachment region beta (S/MARbeta), an ATC-rich DNA sequence located upstream of the TCR beta enhancer. Represses cyclin D1 transcription by recruiting HDAC1 to its promoter, thereby diminishing H3K9ac, H3S10ph and H4K8ac levels. Promotes TP53 'Ser-15' phosphorylation and nuclear accumulation, which causes cell cycle arrest (By similarity). {ECO:0000250, ECO:0000269|PubMed:16166625}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Regulation of TP53 Activity through Association with Co-factors;Regulation of TP53 Activity;Transcriptional Regulation by TP53 (Consensus)

Recessive Scores

• pRec: 0.134

Intolerance Scores

• loftool: 0.0438
• rvis_EVS: -0.82
• rvis_percentile_EVS: 11.77

Haploinsufficiency Scores

• pHI: 0.645
• hipred: Y
• hipred_score: 0.783
• ghis: 0.466

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.986

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Banp

Gene ontology

• Biological process: chromatin organization;cell cycle;multicellular organism development;protein localization to nucleus;negative regulation of protein catabolic process;positive regulation of transcription, DNA-templated;regulation of signal transduction by p53 class mediator
• Cellular component: nucleoplasm;nuclear body
• Molecular function: p53 binding;DNA binding;protein binding