ABTB3

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

Basic information

Region (hg38): 12:107318420-107659642

Previous symbols: [ "BTBD11" ]

Links

ENSG00000151136 ∙ NCBI:121551 ∙ ∙ HGNC:23844 ∙ Uniprot:A6QL63 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ABTB3 gene.

• Inborn genetic diseases (22 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABTB3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3		3
missense			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	22	3	0

Variants in ABTB3

This is a list of pathogenic ClinVar variants found in the ABTB3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-107319038-A-G		not specified	Uncertain significance (Aug 12, 2021)
12-107319067-C-G		not specified	Uncertain significance (Aug 17, 2022)
12-107319068-C-G		not specified	Uncertain significance (Feb 28, 2023)
12-107319088-A-G		Malignant tumor of prostate	Uncertain significance (-)
12-107319206-G-C		not specified	Uncertain significance (Feb 15, 2023)
12-107319215-C-G		not specified	Uncertain significance (Sep 22, 2023)
12-107319275-G-C		not specified	Uncertain significance (Aug 11, 2022)
12-107319282-C-T			Likely benign (Sep 01, 2022)
12-107319296-C-T		not specified	Likely benign (Dec 08, 2023)
12-107319305-G-A		not specified	Uncertain significance (Jun 21, 2023)
12-107319311-T-G		not specified	Uncertain significance (Sep 15, 2021)
12-107319316-A-G		not specified	Uncertain significance (Aug 02, 2021)
12-107319379-G-T		not specified	Uncertain significance (Mar 17, 2023)
12-107319398-G-C		not specified	Uncertain significance (Jun 24, 2022)
12-107319436-A-C		not specified	Uncertain significance (Oct 03, 2022)
12-107319466-G-T		not specified	Uncertain significance (May 27, 2022)
12-107319482-C-T		not specified	Uncertain significance (Nov 09, 2021)
12-107319485-C-A		not specified	Uncertain significance (Jun 27, 2022)
12-107319583-C-T		not specified	Uncertain significance (May 26, 2023)
12-107319653-C-T		not specified	Uncertain significance (Jul 14, 2023)
12-107319727-G-T		not specified	Uncertain significance (Jan 18, 2023)
12-107319740-G-T		not specified	Uncertain significance (Dec 16, 2023)
12-107319754-C-G		not specified	Uncertain significance (Jan 26, 2022)
12-107319758-G-A		not specified	Uncertain significance (Nov 09, 2021)
12-107319781-G-C		not specified	Uncertain significance (Aug 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABTB3	protein_coding	protein_coding	ENST00000280758	17	341230

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000672	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.22	468	624	0.750	0.0000341	7101
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000871	0.0000871
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000441	0.0000352
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000661	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.123

Intolerance Scores

• loftool: 0.338
• rvis_EVS: -0.46
• rvis_percentile_EVS: 23.63

Haploinsufficiency Scores

• pHI: 0.424
• hipred: Y
• hipred_score: 0.774
• ghis: 0.500

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.321

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Btbd11

Gene ontology

• Biological process: SMAD protein signal transduction
• Cellular component: integral component of membrane
• Molecular function: protein heterodimerization activity