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GeneBe

BGN

biglycan, the group of Small leucine rich repeat proteoglycans

Basic information

Region (hg38): X:153494979-153509546

Links

ENSG00000182492NCBI:633OMIM:301870HGNC:1044Uniprot:P21810AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Meester-Loeys syndromeXLCardiovascularAmong other features, the condition can include early-onset aortic aneurysm, and awareness may allow erly diagnosis and managementCardiovascular; Craniofacial; Musculoskeletal; Neurologic8064814; 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
clinvar
58
clinvar
4
clinvar
64
missense
1
clinvar
107
clinvar
5
clinvar
113
nonsense
2
clinvar
2
start loss
0
frameshift
3
clinvar
1
clinvar
4
inframe indel
2
clinvar
2
splice donor/acceptor (+/-2bp)
2
clinvar
2
splice region
8
11
1
20
non coding
22
clinvar
19
clinvar
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)1289069
X-153504412-G-A Benign (Mar 29, 2019)1276181
X-153504606-C-G Likely benign (Nov 05, 2018)1316494
X-153504635-T-C Uncertain significance (Jan 26, 2022)2089480
X-153504636-G-A Familial thoracic aortic aneurysm and aortic dissection • Meester-Loeys syndrome Likely pathogenic (Mar 01, 2021)265794
X-153504647-C-T Uncertain significance (Jan 09, 2024)2177021
X-153504648-G-A X-linked spondyloepimetaphyseal dysplasia Uncertain significance (Jan 29, 2024)1033440
X-153504649-C-T Cardiovascular phenotype Likely benign (Apr 11, 2023)2564953
X-153504652-C-A BGN-related condition Uncertain significance (Apr 07, 2023)2630447
X-153504652-C-T Likely benign (Oct 04, 2022)1930858
X-153504653-G-A Cardiovascular phenotype Uncertain significance (Jan 18, 2024)1445098
X-153504657-C-T Uncertain significance (Aug 18, 2021)1465633
X-153504658-T-C Likely benign (Dec 25, 2023)2808483
X-153504658-T-G Likely benign (Feb 06, 2022)2094133
X-153504659-C-T Cardiovascular phenotype Likely benign (Apr 07, 2023)2564952
X-153504671-AG-A Likely pathogenic (Nov 28, 2018)817331
X-153504683-C-T Uncertain significance (Jul 25, 2023)1925100
X-153504689-G-GAA Likely pathogenic (Jul 04, 2018)636703
X-153504696-G-C Uncertain significance (Jan 18, 2024)3000651
X-153504699-G-C Uncertain significance (Aug 08, 2020)1013933
X-153504703-C-G Uncertain significance (Jan 03, 2020)1224409
X-153504706-G-A Familial aortopathy Likely pathogenic (Mar 23, 2023)2501127
X-153504721-C-G BGN-related condition Uncertain significance (Jul 17, 2023)1490325
X-153504722-G-A Uncertain significance (Nov 24, 2022)3004629
X-153504722-G-T Uncertain significance (Jan 23, 2024)3006069

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
BGNprotein_codingprotein_codingENST00000331595 714616
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.4520.542125732321257370.0000199
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.7141411670.8450.00001462421
Missense in Polyphen4468.6220.641191070
Synonymous-0.8268273.01.120.00000649742
Loss of Function2.3229.880.2027.05e-7167

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.0001250.0000924
European (Non-Finnish)0.00003740.0000264
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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