BTG3

protein-coding

BTG anti-proliferation factor 3, 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 might play a role in neurogenesis in the central nervous system. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2008]

MANE transcript

NM_006806.5

Inheritance

—

ClinVar variants

U:19

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.08

Max pathogenic AF

—

Genomic locus

chr21:17,593,653-17,612,945

External References & Databases

Ensembl (ENSG00000154640)

Transcript & Mutation Effects

hg38 • Region Span ~19.3 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 BTG3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 33

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006806.5. 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						0
missense			18 clinvar			18
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	19	0	0	19

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 63 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006806.5	RefSeq	NP_006797.3	4	MANE Select
ENST00000348354.7	Ensembl	ENSP00000284879.8	4	MANE Select
NM_001130914.2	RefSeq	NP_001124386.1	5	Standard
ENST00000339775.10	Ensembl	ENSP00000344609.6	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

RNA degradation - Homo sapiens (human)

Biological Process

negative regulation of cell population proliferation
negative regulation of mitotic cell cycle

Molecular Function

protein binding

Cellular Component

nucleus
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000339775
Coding exons: 5
Length: 19295
Individuals with no LoFs: 125739
Homozygous LoFs: 0
Heterozygous LoFs: 5
Defined: 125744
p: 0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.86	88	153	0.576	0.00000781	1934
Missense (PolyPhen)		12	43.187	0.27786		542
Synonymous	0.600	47	52.5	0.895	0.00000270	554
Loss of Function	2.99	1	12.3	0.0810	6.51e-7	169

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Overexpression impairs serum-induced cell cycle progression from the G0/G1 to S phase.;

Recessive Scores

pRec: 0.133

Intolerance Scores

LoFtool: 0.112
RVIS EVS: -0.16
RVIS percentile EVS: 41.25

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.802

Gene Damage Prediction

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