BSX

brain specific homeobox, the group of NKL subclass homeoboxes and pseudogenes

Basic information

Region (hg38): 11:122977569-122981834

Links

ENSG00000188909 ∙ NCBI:390259 ∙ OMIM:611074 ∙ HGNC:20450 ∙ Uniprot:Q3C1V8 ∙ 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 BSX gene.

• Inborn genetic diseases (10 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BSX 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	2	3
missense			10		1	11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	1	3

Variants in BSX

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

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

Position	Type	Phenotype	Significance	ClinVar
11-122977657-C-G		not specified	Uncertain significance (May 27, 2022)
11-122977658-G-T			Benign (Jun 12, 2018)
11-122977661-C-A			Benign (Jun 14, 2018)
11-122977682-C-T			Likely benign (Jun 01, 2020)
11-122977684-C-G		not specified	Uncertain significance (Aug 22, 2023)
11-122977695-T-C		not specified	Uncertain significance (Sep 15, 2021)
11-122977740-A-G		not specified	Uncertain significance (Nov 22, 2022)
11-122977756-C-T		not specified	Uncertain significance (Oct 22, 2021)
11-122977783-G-A		not specified	Uncertain significance (Jun 22, 2023)
11-122977785-G-C		not specified	Uncertain significance (Mar 23, 2023)
11-122977815-G-A		not specified	Uncertain significance (Sep 30, 2021)
11-122977831-C-T		not specified	Uncertain significance (Oct 05, 2023)
11-122977848-T-G		not specified	Uncertain significance (Nov 08, 2022)
11-122979270-G-A			Benign (Jul 26, 2018)
11-122981502-G-A		not specified	Uncertain significance (Dec 27, 2023)
11-122981502-G-T		not specified	Uncertain significance (Feb 05, 2024)
11-122981640-G-A		not specified	Uncertain significance (Aug 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BSX	protein_coding	protein_coding	ENST00000343035	3	4151

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00791	0.799	124613	0	180	124793	0.000721

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.484	115	131	0.881	0.00000603	1466
Missense in Polyphen		23	36.511	0.62995		416
Synonymous	-0.351	62	58.6	1.06	0.00000279	500
Loss of Function	1.01	4	6.85	0.584	2.99e-7	80

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00237	0.00188
Ashkenazi Jewish	0.000545	0.000497
East Asian	0.000193	0.000167
Finnish	0.00123	0.00102
European (Non-Finnish)	0.00109	0.000883
Middle Eastern	0.000193	0.000167
South Asian	0.000131	0.000131
Other	0.00248	0.00215

dbNSFP

Source: dbNSFP

• Function: FUNCTION: DNA binding protein that function as transcriptional activator. Is essential for normal postnatal growth and nursing. Is an essential factor for neuronal neuropeptide Y and agouti- related peptide function and locomotory behavior in the control of energy balance (By similarity). {ECO:0000250}.

Intolerance Scores

• loftool: 0.361
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.56

Haploinsufficiency Scores

• pHI: 0.190
• hipred: Y
• hipred_score: 0.580

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.435

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bsx
• Phenotype: normal phenotype; reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype

Zebrafish Information Network

• Gene name: bsx
• Affected structure: pinealocyte
• Phenotype tag: abnormal
• Phenotype quality: decreased occurrence

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;locomotory behavior;eating behavior;positive regulation of transcription by RNA polymerase II;mammary gland involution
• Cellular component: nucleus;transcription factor complex
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;sequence-specific DNA binding