BTBD9

BTB domain containing 9, the group of BTB domain containing

Basic information

Region (hg38): 6:38168450-38640148

Links

ENSG00000183826 ∙ NCBI:114781 ∙ OMIM:611237 ∙ HGNC:21228 ∙ Uniprot:Q96Q07 ∙ 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 BTBD9 gene.

• Inborn genetic diseases (27 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BTBD9 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	2
missense			27			27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	1	1

Variants in BTBD9

This is a list of pathogenic ClinVar variants found in the BTBD9 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-38175019-G-C		not specified	Uncertain significance (Jun 22, 2021)
6-38175055-G-A		not specified	Uncertain significance (Oct 05, 2021)
6-38175136-T-A		not specified	Uncertain significance (Apr 07, 2022)
6-38192551-G-A		not specified	Uncertain significance (May 27, 2022)
6-38256440-T-C		not specified	Uncertain significance (Jun 18, 2021)
6-38256473-C-T		not specified	Uncertain significance (Apr 17, 2023)
6-38288300-C-T		not specified	Uncertain significance (Oct 06, 2021)
6-38288438-T-C		not specified	Uncertain significance (Mar 22, 2023)
6-38288452-T-G		not specified	Uncertain significance (Sep 16, 2021)
6-38345014-T-G		not specified	Uncertain significance (Jul 06, 2021)
6-38577609-C-T		not specified	Uncertain significance (Oct 04, 2022)
6-38577662-T-G			Likely benign (Mar 29, 2018)
6-38577676-A-T		not specified	Uncertain significance (Nov 08, 2022)
6-38577691-T-C		not specified	Uncertain significance (Apr 22, 2022)
6-38577699-T-A		not specified	Uncertain significance (Mar 23, 2023)
6-38580227-C-T		not specified	Uncertain significance (Dec 26, 2023)
6-38580247-T-C		not specified	Uncertain significance (May 09, 2023)
6-38580291-C-T		not specified	Uncertain significance (Oct 28, 2023)
6-38580296-C-T		not specified	Uncertain significance (Oct 20, 2023)
6-38592656-A-C		not specified	Uncertain significance (Mar 02, 2023)
6-38592673-C-T			Benign (Dec 31, 2019)
6-38592795-C-T		not specified	Uncertain significance (Jan 26, 2022)
6-38594028-C-A		not specified	Uncertain significance (Apr 13, 2023)
6-38594043-A-G		not specified	Uncertain significance (Sep 19, 2022)
6-38594044-A-T		not specified	Uncertain significance (Sep 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BTBD9	protein_coding	protein_coding	ENST00000481247	10	471698

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.07e-9	0.971	124933	0	50	124983	0.000200

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.93	251	353	0.711	0.0000200	4022
Missense in Polyphen		25	48.377	0.51677		582
Synonymous	-0.988	143	129	1.11	0.00000690	1172
Loss of Function	2.14	18	30.8	0.584	0.00000176	348

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000448	0.000446
Ashkenazi Jewish	0.00	0.00
East Asian	0.000167	0.000167
Finnish	0.00	0.00
European (Non-Finnish)	0.000266	0.000238
Middle Eastern	0.000167	0.000167
South Asian	0.000164	0.000163
Other	0.000330	0.000329

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.122

Intolerance Scores

• loftool: 0.479
• rvis_EVS: -0.96
• rvis_percentile_EVS: 9.09

Haploinsufficiency Scores

• pHI: 0.311
• hipred: Y
• hipred_score: 0.554
• ghis: 0.625

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Btbd9
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); skeleton phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: btbd9
• Affected structure: trunk
• Phenotype tag: abnormal
• Phenotype quality: curved dorsal

Gene ontology

• Biological process: long-term memory;adult locomotory behavior;serotonin metabolic process;circadian sleep/wake cycle, non-REM sleep;circadian behavior;sensory perception of temperature stimulus;multicellular organismal iron ion homeostasis;regulation of synaptic vesicle endocytosis