BTBD3

BTB domain containing 3, the group of BTB domain containing

Basic information

Region (hg38): 20:11890723-11926609

Links

ENSG00000132640 ∙ NCBI:22903 ∙ OMIM:615566 ∙ HGNC:15854 ∙ Uniprot:Q9Y2F9 ∙ 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 BTBD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BTBD3 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					1	1
missense			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	8	0	1

Variants in BTBD3

This is a list of pathogenic ClinVar variants found in the BTBD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-11918298-A-G		not specified	Uncertain significance (May 14, 2024)
20-11918337-C-T		not specified	Uncertain significance (Jun 03, 2022)
20-11918343-A-G		not specified	Uncertain significance (Jul 26, 2024)
20-11918496-A-C		not specified	Uncertain significance (May 29, 2024)
20-11918513-G-A		not specified	Uncertain significance (Jul 02, 2024)
20-11918520-A-G		not specified	Uncertain significance (Dec 19, 2022)
20-11918540-A-G		not specified	Uncertain significance (Mar 18, 2024)
20-11918546-A-G		not specified	Uncertain significance (Sep 23, 2023)
20-11918559-C-T		not specified	Uncertain significance (Oct 06, 2024)
20-11918564-C-G		not specified	Uncertain significance (Dec 27, 2022)
20-11919826-G-A		not specified	Uncertain significance (Mar 22, 2022)
20-11922707-A-C		not specified	Uncertain significance (Aug 05, 2024)
20-11922739-T-A		not specified	Uncertain significance (Aug 02, 2022)
20-11923006-G-A			Benign (Feb 19, 2019)
20-11923092-A-G		not specified	Uncertain significance (Nov 12, 2021)
20-11923226-C-T		not specified	Uncertain significance (Oct 08, 2024)
20-11923394-G-A		not specified	Uncertain significance (Apr 26, 2024)
20-11923491-C-T		not specified	Uncertain significance (Oct 30, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BTBD3	protein_coding	protein_coding	ENST00000405977	4	35887

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.128	0.871	125729	0	11	125740	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.64	170	299	0.569	0.0000164	3478
Missense in Polyphen		16	61.547	0.25997		757
Synonymous	0.465	103	109	0.943	0.00000588	993
Loss of Function	2.91	5	18.5	0.271	9.48e-7	226

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000441	0.0000352
Middle Eastern	0.000109	0.000109
South Asian	0.0000982	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a key regulator of dendritic field orientation during development of sensory cortex. Also directs dendrites toward active axon terminals when ectopically expressed (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.116

Intolerance Scores

• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.92

Haploinsufficiency Scores

• pHI: 0.247
• hipred: N
• hipred_score: 0.476
• ghis: 0.563

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0524

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Btbd3

Gene ontology

• Biological process: cerebral cortex development;neurogenesis;dendrite morphogenesis
• Cellular component: nucleus;cytosol