ABTB3

protein-coding

ankyrin repeat and BTB domain containing 3, the group of BTB domain containing|Ankyrin repeat domain containing

Gene summary

Predicted to enable PDZ domain binding activity and protein heterodimerization activity. Predicted to act upstream of or within exploration behavior; glutamatergic synaptic transmission; and protein stabilization. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

BTBD11

MANE transcript

NM_001018072.2

Inheritance

—

ClinVar variants

U:161B:6

Top phenotype

Prostate cancer

gnomAD constraint

pLI —, LoF o/e 0.09

Max pathogenic AF

—

Genomic locus

chr12:107,318,421-107,659,642

External References & Databases

Ensembl (ENSG00000151136)

Transcript & Mutation Effects

hg38 • Region Span ~341.2 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 ABTB3 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 150

not providedTotal: 7

Prostate cancerTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001018072.2. 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				5 clinvar		5
missense			155 clinvar	1 clinvar		156
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	161	6	0	167

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001018072.2	RefSeq	NP_001018082.1	17	MANE Select
ENST00000280758.10	Ensembl	ENSP00000280758.5	17	MANE Select
NM_001017523.2	RefSeq	NP_001017523.1	15	Standard
NM_001347943.2	RefSeq	NP_001334872.1	15	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

SMAD protein signal transduction

Molecular Function

protein heterodimerization activity

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000280758
Coding exons: 17
Length: 341230
Individuals with no LoFs: 125738
Homozygous LoFs: 0
Heterozygous LoFs: 10
Defined: 125748
p: 0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.22	468	624	0.750	0.0000341	7101
Missense (PolyPhen)		151	241.37	0.62559		2684
Synonymous	0.775	265	282	0.941	0.0000170	2253
Loss of Function	5.65	4	44.9	0.0891	0.00000214	520

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000044	0.000035	rare
South Asian	0.000066	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.123

Intolerance Scores

LoFtool: 0.338
RVIS EVS: -0.46
RVIS percentile EVS: 23.63

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.321

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High