ABTB1

protein-coding

ankyrin repeat and BTB domain containing 1, the group of Ankyrin repeat domain containing|BTB domain containing

Gene summary

This gene encodes a protein with an ankyrin repeat region and two BTB/POZ domains, which are thought to be involved in protein-protein interactions. Expression of this gene is activated by the phosphatase and tensin homolog, a tumor suppressor. Alternate splicing results in three transcript variants. [provided by RefSeq, Mar 2010]

MANE transcript

NM_172027.3

Inheritance

—

ClinVar variants

U:107B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.47

Max pathogenic AF

—

Genomic locus

chr3:127,672,935-127,680,926

External References & Databases

Ensembl (ENSG00000114626)

Transcript & Mutation Effects

hg38 • Region Span ~8.0 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 ABTB1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 109

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_172027.3. 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			102 clinvar	7 clinvar		109
nonsense			1 clinvar	1 clinvar		2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	107	9	0	116

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 58 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_172027.3	RefSeq	NP_742024.1	12	MANE Select
ENST00000232744.13	Ensembl	ENSP00000232744.8	12	MANE Select
NM_032548.4	RefSeq	NP_115937.1	8	Standard
ENST00000453791.6	Ensembl	ENSP00000412684.2	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

translational elongation

Molecular Function

translation elongation factor activity
protein binding

Cellular Component

ubiquitin ligase complex
nucleolus
cytosol
plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000232744
Coding exons: 12
Length: 7991
Individuals with no LoFs: 124664
Homozygous LoFs: 2
Heterozygous LoFs: 1081
Defined: 125747
p: 0.00432

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.345	298	315	0.945	0.0000220	3073
Missense (PolyPhen)		73	96.009	0.76035		977
Synonymous	-1.00	153	138	1.11	0.0000103	961
Loss of Function	2.51	12	25.7	0.467	0.00000143	268

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0016	0.0015	notable
Latino/Admixed American	0.0025	0.0025	notable
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00011	0.00011	rare
Finnish	0.0082	0.0079	notable
European (Non-Finnish)	0.0063	0.0061	notable
South Asian	0.0031	0.0030	notable
Other	0.0030	0.0029	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May act as a mediator of the PTEN growth-suppressive signaling pathway. May play a role in developmental processes. {ECO:0000269|PubMed:10891360, ECO:0000269|PubMed:11494141}.;

Recessive Scores

pRec: 0.113

Intolerance Scores

LoFtool: 0.476
RVIS EVS: -0.95
RVIS percentile EVS: 9.27

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.564

Gene Damage Prediction

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