BANP

protein-coding

BTG3 associated nuclear protein, the group of BEN domain containing

Gene summary

This gene encodes a protein that binds to matrix attachment regions. The protein forms a complex with p53 and negatively regulates p53 transcription, and functions as a tumor suppressor and cell cycle regulator. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2010]

MANE transcript

NM_001386991.1

Inheritance

—

ClinVar variants

U:72B:2

Top phenotype

Ependymoma

gnomAD constraint

pLI —, LoF o/e 0.11

Max pathogenic AF

—

Genomic locus

chr16:87,949,244-88,077,318

External References & Databases

Ensembl (ENSG00000172530)

Transcript & Mutation Effects

hg38 • Region Span ~128.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to BANP variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 64

not providedTotal: 3

EpendymomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001386991.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar	1 clinvar	3
missense			69 clinvar			69
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	72	1	1	74

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 200 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001386991.1	RefSeq	NP_001373920.1	13	MANE Select
ENST00000682872.1	Ensembl	ENSP00000507916.1	13	MANE Select
NM_001173539.2	RefSeq	NP_001167010.1	12	Standard
NM_001173540.2	RefSeq	NP_001167011.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Gene expression (Transcription)
Generic Transcription Pathway
RNA Polymerase II Transcription
Regulation of TP53 Activity through Association with Co-factors
Regulation of TP53 Activity

Biological Process

chromatin organization
cell cycle
multicellular organism development
protein localization to nucleus
negative regulation of protein catabolic process

Molecular Function

p53 binding
DNA binding
protein binding

Cellular Component

nucleoplasm
nuclear body

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000393207
Coding exons: 13
Length: 128075
Individuals with no LoFs: 125742
Homozygous LoFs: 0
Heterozygous LoFs: 5
Defined: 125747
p: 0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.43	219	346	0.633	0.0000238	3370
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000091	0.0000088	rare
South Asian	0.000067	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.134

Intolerance Scores

LoFtool: 0.0438
RVIS EVS: -0.82
RVIS percentile EVS: 11.77

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.986

Gene Damage Prediction

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