BTG2

protein-coding

BTG anti-proliferation factor 2, the group of BTG/Tob family

Gene summary

The protein encoded by this gene is a member of the BTG/Tob family. This family has structurally related proteins that appear to have antiproliferative properties. This encoded protein is involved in the regulation of the G1/S transition of the cell cycle. [provided by RefSeq, Jul 2008]

MANE transcript

NM_006763.3

Inheritance

—

ClinVar variants

U:21B:2

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.61

Max pathogenic AF

—

Genomic locus

chr1:203,305,491-203,309,602

External References & Databases

Ensembl (ENSG00000159388)

Transcript & Mutation Effects

hg38 • Region Span ~4.1 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 BTG2 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 14

EBV-positive nodal T- and NK-cell lymphomaTotal: 3

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006763.3. 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		2
missense			17 clinvar	1 clinvar		18
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	21	2	0	23

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006763.3	RefSeq	NP_006754.1	2	MANE Select
ENST00000290551.5	Ensembl	ENSP00000290551.4	2	MANE Select
ENST00000475157.1	Ensembl	ENSP00000433553.1	2	Standard
ENST00001119532.1	Ensembl	ENSP00000789337.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

RNA degradation - Homo sapiens (human)
Spinal Cord Injury
TP53 Regulates Transcription of Cell Cycle Genes
Gene expression (Transcription)
btg family proteins and cell cycle regulation

Biological Process

negative regulation of transcription by RNA polymerase II
DNA repair
protein methylation
cellular response to DNA damage stimulus
DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest

Molecular Function

DNA-binding transcription repressor activity, RNA polymerase II-specific
protein binding

Cellular Component

nucleus
cytoplasm
cytosol
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000290551
Coding exons: 2
Length: 4112
Individuals with no LoFs: 125726
Homozygous LoFs: 0
Heterozygous LoFs: 8
Defined: 125734
p: 0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.718	71	90.2	0.787	0.00000467	1005
Missense (PolyPhen)		15	34.988	0.42872		373
Synonymous	-0.896	46	38.9	1.18	0.00000218	311
Loss of Function	0.815	3	4.96	0.605	2.12e-7	55

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000044	0.000044	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Anti-proliferative protein; the function is mediated by association with deadenylase subunits of the CCR4-NOT complex. Activates mRNA deadenylation in a CNOT6 and CNOT7-dependent manner. In vitro can inhibit deadenylase activity of CNOT7 and CNOT8. Involved in cell cycle regulation. Could be involved in the growth arrest and differentiation of the neuronal precursors (By similarity). Modulates transcription regulation mediated by ESR1. Involved in mitochondrial depolarization and neurite outgrowth. {ECO:0000250, ECO:0000269|PubMed:12771185, ECO:0000269|PubMed:15788397, ECO:0000269|PubMed:18337750, ECO:0000269|PubMed:18773938, ECO:0000269|PubMed:23236473}.;

Recessive Scores

pRec: 0.111

Intolerance Scores

LoFtool: 0.318
RVIS EVS: -0.21
RVIS percentile EVS: 38.28

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.942

Gene Damage Prediction

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