BGN

biglycan, the group of Small leucine rich repeat proteoglycans

Basic information

Region (hg38): X:153494979-153509546

Links

ENSG00000182492 ∙ NCBI:633 ∙ OMIM:301870 ∙ HGNC:1044 ∙ Uniprot:P21810 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Meester-Loeys syndrome (Limited), mode of inheritance: XL
• Meester-Loeys syndrome (Strong), mode of inheritance: XL
• X-linked spondyloepimetaphyseal dysplasia (Limited), mode of inheritance: XL
• Meester-Loeys syndrome (Moderate), mode of inheritance: XL
• X-linked spondyloepimetaphyseal dysplasia (Supportive), mode of inheritance: XL
• X-linked spondyloepimetaphyseal dysplasia (Strong), mode of inheritance: XL
• familial thoracic aortic aneurysm and aortic dissection (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Meester-Loeys syndrome	XL	Cardiovascular	Among other features, the condition can include early-onset aortic aneurysm, and awareness may allow erly diagnosis and management	Cardiovascular; Craniofacial; Musculoskeletal; Neurologic	8064814; 27236923; 27632686

ClinVar

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

• not provided (201 variants)
• Cardiovascular phenotype (94 variants)
• not specified (18 variants)
• X-linked spondyloepimetaphyseal dysplasia (10 variants)
• Meester-Loeys syndrome (10 variants)
• Inborn genetic diseases (6 variants)
• X-linked spondyloepimetaphyseal dysplasia;Meester-Loeys syndrome (4 variants)
• BGN-related condition (4 variants)
• Familial thoracic aortic aneurysm and aortic dissection (2 variants)
• Familial aortopathy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BGN 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			2	58	4	64
missense		1	107	5		113
nonsense		2				2
start loss						0
frameshift		3	1			4
inframe indel			2			2
splice donor/acceptor (+/-2bp)			2			2
splice region			8	11	1	20
non coding				22	19	41
Total	0	6	114	85	23

Variants in BGN

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

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

Position	Type	Phenotype	Significance	ClinVar
X-153504296-A-G			Benign (Sep 06, 2018)
X-153504412-G-A			Benign (Mar 29, 2019)
X-153504606-C-G			Likely benign (Nov 05, 2018)
X-153504635-T-C			Uncertain significance (Jan 26, 2022)
X-153504636-G-A		Familial thoracic aortic aneurysm and aortic dissection • Meester-Loeys syndrome	Likely pathogenic (Mar 01, 2021)
X-153504647-C-T			Uncertain significance (Jan 09, 2024)
X-153504648-G-A		X-linked spondyloepimetaphyseal dysplasia • Cardiovascular phenotype	Uncertain significance (Jan 29, 2024)
X-153504649-C-T		Cardiovascular phenotype	Likely benign (Apr 11, 2023)
X-153504652-C-A		BGN-related disorder	Uncertain significance (Apr 07, 2023)
X-153504652-C-T			Likely benign (Oct 04, 2022)
X-153504653-G-A		Cardiovascular phenotype	Uncertain significance (Jan 18, 2024)
X-153504657-C-T			Uncertain significance (Aug 18, 2021)
X-153504658-T-C			Likely benign (Dec 25, 2023)
X-153504658-T-G			Likely benign (Feb 06, 2022)
X-153504659-C-T		Cardiovascular phenotype	Likely benign (Apr 07, 2023)
X-153504671-AG-A			Likely pathogenic (Nov 28, 2018)
X-153504675-AG-A		Meester-Loeys syndrome	Likely pathogenic (Oct 20, 2023)
X-153504683-C-T			Uncertain significance (Jul 25, 2023)
X-153504689-G-GAA		Meester-Loeys syndrome	Likely pathogenic (Oct 20, 2023)
X-153504696-G-C			Uncertain significance (Jan 18, 2024)
X-153504699-G-C			Uncertain significance (Aug 08, 2020)
X-153504703-C-G			Uncertain significance (Jan 03, 2020)
X-153504706-G-A		Familial aortopathy • Meester-Loeys syndrome	Likely pathogenic (Oct 20, 2023)
X-153504721-C-G		BGN-related disorder	Uncertain significance (Jul 17, 2023)
X-153504722-G-A			Uncertain significance (Nov 24, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BGN	protein_coding	protein_coding	ENST00000331595	7	14616

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.452	0.542	125732	3	2	125737	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.714	141	167	0.845	0.0000146	2421
Missense in Polyphen		44	68.622	0.64119		1070
Synonymous	-0.826	82	73.0	1.12	0.00000649	742
Loss of Function	2.32	2	9.88	0.202	7.05e-7	167

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000125	0.0000924
European (Non-Finnish)	0.0000374	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in collagen fiber assembly. {ECO:0000250}.
• Disease: DISEASE: Meester-Loeys syndrome (MRLS) [MIM:300989]: An X-linked, thoracic aortic aneurysm syndrome characterized by early-onset, severe aortic aneurysm and dissection. Other recurrent findings include hypertelorism, pectus deformity, joint hypermobility, contractures, and mild skeletal dysplasia. {ECO:0000269|PubMed:27632686}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Spondyloepimetaphyseal dysplasia, X-linked (SEMDX) [MIM:300106]: A X-linked recessive bone disease characterized by severe short-trunk dwarfism, brachydactyly, metaphyseal flaring of lower extremities, short and broad long bone diaphyses, moderate platyspondyly, normal facies, and normal intelligence. {ECO:0000269|PubMed:27236923}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Metabolism of carbohydrates;A tetrasaccharide linker sequence is required for GAG synthesis;Heparan sulfate/heparin (HS-GAG) metabolism;Chondroitin sulfate biosynthesis;Dermatan sulfate biosynthesis;Chondroitin sulfate/dermatan sulfate metabolism;Glycosaminoglycan metabolism;Extracellular matrix organization;Metabolism;Integrin;ECM proteoglycans;Endogenous TLR signaling (Consensus)

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.0632
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.91

Haploinsufficiency Scores

• pHI: 0.965
• hipred: Y
• hipred_score: 0.746
• ghis: 0.538

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: Bgn
• Phenotype: growth/size/body region 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); homeostasis/metabolism phenotype; cellular phenotype; craniofacial phenotype; muscle phenotype; limbs/digits/tail phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; immune system phenotype

Gene ontology

• Biological process: blood vessel remodeling;biological_process;peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan;extracellular matrix organization;chondroitin sulfate biosynthetic process;chondroitin sulfate catabolic process;dermatan sulfate biosynthetic process
• Cellular component: extracellular region;Golgi lumen;cell surface;transport vesicle;extracellular matrix;sarcolemma;lysosomal lumen;collagen-containing extracellular matrix;extracellular exosome
• Molecular function: extracellular matrix structural constituent;glycosaminoglycan binding;extracellular matrix structural constituent conferring compression resistance;extracellular matrix binding