BST1

bone marrow stromal cell antigen 1, the group of CD molecules

Basic information

Region (hg38): 4:15703064-15738313

Links

ENSG00000109743 ∙ NCBI:683 ∙ OMIM:600387 ∙ HGNC:1118 ∙ Uniprot:Q10588 ∙ 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 BST1 gene.

• Inborn genetic diseases (15 variants)
• not provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BST1 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			14	2	3	19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	3	4

Variants in BST1

This is a list of pathogenic ClinVar variants found in the BST1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-15703170-C-G		not specified	Uncertain significance (Oct 02, 2023)
4-15703202-C-T		not specified	Uncertain significance (Jan 19, 2024)
4-15703236-G-C		not specified	Likely benign (Oct 20, 2023)
4-15703287-T-C		not specified	Uncertain significance (Jun 09, 2022)
4-15703301-G-A		not specified	Uncertain significance (Oct 14, 2023)
4-15703328-C-G		not specified	Uncertain significance (May 11, 2022)
4-15705586-C-T		not specified	Uncertain significance (Dec 18, 2023)
4-15705627-A-G			Benign (Dec 31, 2019)
4-15705635-A-C		not specified	Uncertain significance (Apr 11, 2023)
4-15707553-G-A		not specified	Uncertain significance (Jul 07, 2022)
4-15707565-C-T			Benign (Jun 13, 2018)
4-15707566-G-A		not specified	Uncertain significance (Aug 13, 2021)
4-15707568-C-T		not specified	Uncertain significance (Jul 15, 2021)
4-15707585-C-G		not specified	Uncertain significance (Jan 31, 2023)
4-15707630-A-G			Benign (Aug 20, 2018)
4-15707635-A-G		not specified	Uncertain significance (May 31, 2022)
4-15711854-C-G		not specified	Likely benign (Jun 06, 2023)
4-15711875-A-G		not specified	Uncertain significance (Dec 13, 2021)
4-15715300-T-C		not specified	Uncertain significance (Sep 13, 2023)
4-15715303-G-C		not specified	Uncertain significance (Oct 03, 2022)
4-15715340-C-T		not specified	Uncertain significance (Apr 10, 2023)
4-15715757-G-A		not specified	Uncertain significance (Oct 22, 2021)
4-15715758-A-G			Likely benign (Jul 29, 2018)
4-15715789-G-A			Likely benign (May 11, 2018)
4-15715792-C-T		not specified	Uncertain significance (Apr 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BST1	protein_coding	protein_coding	ENST00000265016	9	35364

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.21e-11	0.101	125621	0	126	125747	0.000501

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.103	173	169	1.02	0.00000930	2036
Missense in Polyphen		55	57.959	0.94895		738
Synonymous	0.739	64	72.0	0.889	0.00000459	614
Loss of Function	0.378	17	18.8	0.906	0.00000114	189

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000798	0.000798
Ashkenazi Jewish	0.00	0.00
East Asian	0.00201	0.00201
Finnish	0.000371	0.000370
European (Non-Finnish)	0.000398	0.000396
Middle Eastern	0.00201	0.00201
South Asian	0.000454	0.000392
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Synthesizes the second messagers cyclic ADP-ribose and nicotinate-adenine dinucleotide phosphate, the former a second messenger that elicits calcium release from intracellular stores. May be involved in pre-B-cell growth. {ECO:0000269|PubMed:11866528}.
• Pathway: Nicotinate and nicotinamide metabolism - Homo sapiens (human);Salivary secretion - Homo sapiens (human);Pancreatic secretion - Homo sapiens (human);Nicotinate and Nicotinamide Metabolism;NAD+ biosynthetic pathways;Neutrophil degranulation;Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins;Vitamin B3 (nicotinate and nicotinamide) metabolism;Innate Immune System;Immune System;Metabolism;Nicotinate Nicotinamide metabolism;Nicotinate metabolism;Metabolism of water-soluble vitamins and cofactors;Metabolism of vitamins and cofactors (Consensus)

Recessive Scores

• pRec: 0.198

Intolerance Scores

• loftool: 0.853
• rvis_EVS: 0.86
• rvis_percentile_EVS: 88.69

Haploinsufficiency Scores

• pHI: 0.127
• hipred: N
• hipred_score: 0.112
• ghis: 0.403

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.515

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bst1
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: regulation of cell-matrix adhesion;regulation of cellular extravasation;humoral immune response;signal transduction;positive regulation of cell population proliferation;NAD metabolic process;positive regulation of B cell proliferation;regulation of actin cytoskeleton organization;neutrophil degranulation;regulation of inflammatory response;regulation of peptidyl-tyrosine phosphorylation;regulation of calcium-mediated signaling;regulation of neutrophil chemotaxis;regulation of superoxide metabolic process;regulation of integrin-mediated signaling pathway
• Cellular component: uropod;extracellular region;plasma membrane;integrin complex;extrinsic component of membrane;anchored component of membrane;specific granule membrane;extracellular exosome
• Molecular function: NAD+ nucleosidase activity;transferase activity;phosphorus-oxygen lyase activity;NAD(P)+ nucleosidase activity;NAD+ nucleotidase, cyclic ADP-ribose generating;ADP-ribosyl cyclase activity;cyclic ADP-ribose hydrolase