SEMDX
MCID: SPN358
MIFTS: 39

Spondyloepimetaphyseal Dysplasia, X-Linked (SEMDX)

Categories: Bone diseases, Fetal diseases, Genetic diseases, Rare diseases
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Aliases & Classifications for Spondyloepimetaphyseal Dysplasia, X-Linked

MalaCards integrated aliases for Spondyloepimetaphyseal Dysplasia, X-Linked:

Name: Spondyloepimetaphyseal Dysplasia, X-Linked 57 73 43 38 71
X-Linked Spondyloepimetaphyseal Dysplasia 11 58 28 5 14
Semdx 57 11 19 73
Semd, X-Linked 57 73
Semd X-Linked 11 19
Spondyloepimetaphyseal Dysplasia X-Linked 19
Spondylo-Epimetaphyseal Dysplasia 19

Characteristics:


Inheritance:

Spondyloepimetaphyseal Dysplasia, X-Linked: X-linked recessive 57
X-Linked Spondyloepimetaphyseal Dysplasia: X-linked recessive 58

OMIM®:

57 (Updated 24-Oct-2022)
Miscellaneous:
pectus carinatum present in obligate carrier mothers
dwarfism not detectable at birth


Classifications:

Orphanet: 58  
Rare bone diseases
Developmental anomalies during embryogenesis


External Ids:

Disease Ontology 11 DOID:0112150
OMIM® 57 300106
SNOMED-CT 68 770603000
ICD10 via Orphanet 32 Q77.7
UMLS via Orphanet 72 C1848097
Orphanet 58 ORPHA93349
MedGen 40 C1848097
UMLS 71 C1848097

Summaries for Spondyloepimetaphyseal Dysplasia, X-Linked

GARD: 19 A rare, genetic primary bone dysplasia disorder characterized by disproportionate short stature with mesomelic short limbs, leg bowing, lumbar lordosis, brachydactyly, joint laxity and a waddling gait. Radiographs show platyspondyly with central protrusion of anterior vertebral bodies, kyphotic angulation and very short long bones with dysplastic epiphyses and flarred, irregular, cupped metaphyses.

MalaCards based summary: Spondyloepimetaphyseal Dysplasia, X-Linked, also known as x-linked spondyloepimetaphyseal dysplasia, is related to spondyloepimetaphyseal dysplasia and osteochondrodysplasia. An important gene associated with Spondyloepimetaphyseal Dysplasia, X-Linked is BGN (Biglycan), and among its related pathways/superpathways are Ciliary landscape and Intraflagellar transport. Affiliated tissues include bone and tongue, and related phenotypes are kyphosis and pectus carinatum

Orphanet: 58 A rare, genetic primary bone dysplasia disorder characterized by disproportionate short stature with mesomelic short limbs, leg bowing, lumbar lordosis, brachydactyly, joint laxity and a waddling gait. Radiographs show platyspondyly with central protrusion of anterior vertebral bodies, kyphotic angulation and very short long bones with dysplastic epiphyses and flarred, irregular, cupped metaphyses.

UniProtKB/Swiss-Prot: 73 An 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.

Disease Ontology: 11 A spondyloepimetaphyseal dysplasia that has material basis in hemizygous mutation in BGN on chromosome Xq28.

More information from OMIM: 300106

Related Diseases for Spondyloepimetaphyseal Dysplasia, X-Linked

Graphical network of the top 20 diseases related to Spondyloepimetaphyseal Dysplasia, X-Linked:



Diseases related to Spondyloepimetaphyseal Dysplasia, X-Linked

Symptoms & Phenotypes for Spondyloepimetaphyseal Dysplasia, X-Linked

Human phenotypes related to Spondyloepimetaphyseal Dysplasia, X-Linked:

30 (show all 35)
# Description HPO Frequency Orphanet Frequency HPO Source Accession
1 kyphosis 30 HP:0002808
2 pectus carinatum 30 HP:0000768
3 disproportionate short-trunk short stature 30 HP:0003521
4 brachydactyly 30 HP:0001156
5 platyspondyly 30 HP:0000926
6 coxa valga 30 HP:0002673
7 hypoplasia of the maxilla 30 HP:0000327
8 short metacarpal 30 HP:0010049
9 short foot 30 HP:0001773
10 narrow pelvis bone 30 HP:0003275
11 lumbar hyperlordosis 30 HP:0002938
12 short palm 30 HP:0004279
13 short clavicles 30 HP:0000894
14 cone-shaped epiphyses of the phalanges of the hand 30 HP:0010230
15 short phalanx of finger 30 HP:0009803
16 long fibula 30 HP:0003085
17 cone-shaped metacarpal epiphyses 30 HP:0006059
18 flat acetabular roof 30 HP:0003180
19 limited elbow extension 30 HP:0001377
20 metaphyseal irregularity 30 HP:0003025
21 hypoplasia of the odontoid process 30 HP:0003311
22 broad metacarpals 30 HP:0001230
23 spondyloepimetaphyseal dysplasia 30 HP:0002651
24 radial deviation of the hand 30 HP:0009486
25 broad phalanx 30 HP:0006009
26 delayed ossification of carpal bones 30 HP:0001216
27 broad long bone diaphyses 30 HP:0006371
28 flared iliac wing 30 HP:0002869
29 anterior wedging of t12 30 HP:0011940
30 posterior rib cupping 30 HP:0000922
31 long ulna 30 HP:0003988
32 cone-shaped distal radial epiphysis 30 HP:0004000
33 anterior wedging of t11 30 HP:0004573
34 prominent styloid process of ulna 30 HP:0004981
35 cone-shaped epiphyses fused within their metaphyses 30 HP:0005066

Symptoms via clinical synopsis from OMIM®:

57 (Updated 24-Oct-2022)
Skeletal Spine:
kyphosis
platyspondyly
lumbar lordosis
mild odontoid hypoplasia
anterior vertebral tongue (infancy)
more
Skeletal Hands:
brachydactyly
short hands
delayed carpal bone age
radial deviation of hands
short, broad metacarpals and phalanges
more
Skeletal:
spondyloepimetaphyseal dysplasia

Neurologic Central Nervous System:
normal intelligence

Skeletal Limbs:
irregular metaphyses
disproportionately long fibulae
moderate limitation of elbow extension
short, broad long bone diaphyses
disproportionately long ulnae
more
Skeletal Skull:
mild maxillary hypoplasia

Chest Ribs Sternum Clavicles And Scapulae:
pectus carinatum
short clavicles
posterior rib cupping

Skeletal Pelvis:
coxa valga
flared iliac wings
horizontal acetabular roof
narrow pelvis
hypoplastic iliac bones
more
Skeletal Feet:
short feet

Head And Neck Face:
normal facies

Growth Height:
severe short-trunked dwarfism (identifiable in early childhood)

Clinical features from OMIM®:

300106 (Updated 24-Oct-2022)

Drugs & Therapeutics for Spondyloepimetaphyseal Dysplasia, X-Linked

Search Clinical Trials, NIH Clinical Center for Spondyloepimetaphyseal Dysplasia, X-Linked

Cochrane evidence based reviews: spondyloepimetaphyseal dysplasia, x-linked

Genetic Tests for Spondyloepimetaphyseal Dysplasia, X-Linked

Genetic tests related to Spondyloepimetaphyseal Dysplasia, X-Linked:

# Genetic test Affiliating Genes
1 X-Linked Spondyloepimetaphyseal Dysplasia 28 BGN

Anatomical Context for Spondyloepimetaphyseal Dysplasia, X-Linked

Organs/tissues related to Spondyloepimetaphyseal Dysplasia, X-Linked:

MalaCards : Bone, Tongue

Publications for Spondyloepimetaphyseal Dysplasia, X-Linked

Articles related to Spondyloepimetaphyseal Dysplasia, X-Linked:

(show all 13)
# Title Authors PMID Year
1
BGN Mutations in X-Linked Spondyloepimetaphyseal Dysplasia. 62 57 5
27236923 2016
2
New X linked spondyloepimetaphyseal dysplasia: report on eight affected males in the same family. 62 57 5
8064814 1994
3
A novel homozygous missense variant in MATN3 causes spondylo-epimetaphyseal dysplasia Matrilin 3 type in a consanguineous family. 62
32470407 2020
4
Biallelic variants p.Arg1133Cys and p.Arg1379Cys in COL2A1: Further delineation of phenotypic spectrum of recessive Type 2 collagenopathies. 62
31755234 2020
5
Functional knockout of the matrilin-3 gene causes premature chondrocyte maturation to hypertrophy and increases bone mineral density and osteoarthritis. 62
16877353 2006
6
Identification of sequence polymorphisms in two sulfation-related genes, PAPSS2 and SLC26A2, and an association analysis with knee osteoarthritis. 62
11558903 2001
7
Spondylo-epimetaphyseal dysplasia: a new X-linked variant with mental retardation. 62
10486082 1999
8
Spondylo-epimetaphyseal dysplasia with joint laxity and severe kyphoscoliosis in an Italian girl. 62
7567245 1995
9
Micromelic dwarfism--humerus, femur, tibia type. Report of a case. 62
8255648 1993
10
Type II collagen defect in two sibs with the Goldblatt syndrome, a chondrodysplasia with dentinogenesis imperfecta, and joint laxity. 62
1481841 1992
11
[Spondyloepimetaphyseal dysplasia. Case report]. 62
2091430 1990
12
Radiographic features of spondylo-epimetaphyseal dysplasia with joint laxity and progressive kyphoscoliosis. Review of 19 cases. 62
6435203 1984
13
Spondylo-epimetaphyseal dysplasia with joint laxity and severe, progressive kyphoscoliosis. A potentially lethal dwarfing disorder. 62
6635864 1983

Variations for Spondyloepimetaphyseal Dysplasia, X-Linked

ClinVar genetic disease variations for Spondyloepimetaphyseal Dysplasia, X-Linked:

5 (show all 14)
# Gene Name Type Significance ClinVarId dbSNP ID Position
1 BGN NM_001711.6(BGN):c.776G>T (p.Gly259Val) SNV Pathogenic
243091 rs879255605 GRCh37: X:152772510-152772510
GRCh38: X:153507052-153507052
2 BGN NM_001711.6(BGN):c.439A>G (p.Lys147Glu) SNV Pathogenic
243090 rs879255604 GRCh37: X:152771408-152771408
GRCh38: X:153505950-153505950
3 ABCD1 NM_000033.4(ABCD1):c.796G>A (p.Gly266Arg) SNV Pathogenic
11299 rs128624218 GRCh37: X:152991517-152991517
GRCh38: X:153726062-153726062
4 ABCD1 NM_000033.4(ABCD1):c.1552C>T (p.Arg518Trp) SNV Pathogenic
11307 rs128624224 GRCh37: X:153005609-153005609
GRCh38: X:153740155-153740155
5 BGN NM_001711.6(BGN):c.955G>A (p.Asp319Asn) SNV Uncertain Significance
1675114 GRCh37: X:152773751-152773751
GRCh38: X:153508293-153508293
6 BGN NM_001711.6(BGN):c.645C>G (p.Ile215Met) SNV Uncertain Significance
1029523 rs2089802360 GRCh37: X:152772066-152772066
GRCh38: X:153506608-153506608
7 BGN NM_001711.6(BGN):c.17G>A (p.Arg6His) SNV Uncertain Significance
1033440 rs781931209 GRCh37: X:152770106-152770106
GRCh38: X:153504648-153504648
8 BGN NM_001711.6(BGN):c.682C>T (p.Pro228Ser) SNV Uncertain Significance
1033441 rs2089804261 GRCh37: X:152772293-152772293
GRCh38: X:153506835-153506835
9 BGN NM_001711.6(BGN):c.238+75A>G SNV Benign
1192382 GRCh37: X:152770402-152770402
GRCh38: X:153504944-153504944
10 BGN NM_001711.6(BGN):c.771-32C>T SNV Benign
1192383 GRCh37: X:152772473-152772473
GRCh38: X:153507015-153507015
11 BGN NM_001711.6(BGN):c.909+115T>C SNV Benign
1192384 GRCh37: X:152772758-152772758
GRCh38: X:153507300-153507300
12 BGN NM_001711.6(BGN):c.257A>G (p.Lys86Arg) SNV Benign
1098726 GRCh37: X:152770714-152770714
GRCh38: X:153505256-153505256
13 BGN NM_001711.6(BGN):c.141G>A (p.Ser47=) SNV Benign
1165870 GRCh37: X:152770230-152770230
GRCh38: X:153504772-153504772
14 BGN NM_001711.6(BGN):c.540C>T (p.Ser180=) SNV Benign
1166521 GRCh37: X:152771509-152771509
GRCh38: X:153506051-153506051

UniProtKB/Swiss-Prot genetic disease variations for Spondyloepimetaphyseal Dysplasia, X-Linked:

73
# Symbol AA change Variation ID SNP ID
1 BGN p.Lys147Glu VAR_076590 rs879255604
2 BGN p.Gly259Val VAR_076591 rs879255605

Expression for Spondyloepimetaphyseal Dysplasia, X-Linked

Search GEO for disease gene expression data for Spondyloepimetaphyseal Dysplasia, X-Linked.

Pathways for Spondyloepimetaphyseal Dysplasia, X-Linked

Pathways related to Spondyloepimetaphyseal Dysplasia, X-Linked according to GeneCards Suite gene sharing:

# Super pathways Score Top Affiliating Genes
1 11.13 IFT57 IFT52 EXOC6B
2 10.69 IFT57 IFT52

GO Terms for Spondyloepimetaphyseal Dysplasia, X-Linked

Cellular components related to Spondyloepimetaphyseal Dysplasia, X-Linked according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 ciliary tip GO:0097542 9.62 IFT57 IFT52
2 ciliary base GO:0097546 9.56 IFT57 IFT52
3 photoreceptor connecting cilium GO:0032391 9.46 IFT57 IFT52
4 intraciliary transport particle B GO:0030992 9.26 IFT57 IFT52
5 dendrite terminus GO:0044292 8.92 IFT57 IFT52

Biological processes related to Spondyloepimetaphyseal Dysplasia, X-Linked according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 intraciliary transport GO:0042073 9.56 IFT57 IFT52
2 keratinocyte proliferation GO:0043616 9.46 IFT57 IFT52
3 negative regulation of keratinocyte proliferation GO:0010839 9.26 IFT57 IFT52
4 intraciliary anterograde transport GO:0035720 8.92 IFT57 IFT52

Sources for Spondyloepimetaphyseal Dysplasia, X-Linked

2 CDC
6 CNVD
8 Cosmic
9 dbSNP
10 DGIdb
16 EFO
17 ExPASy
18 FMA
19 GARD
27 GO
28 GTR
29 HMDB
30 HPO
31 ICD10
32 ICD10 via Orphanet
33 ICD11
34 ICD9CM
35 IUPHAR
36 LifeMap
38 LOVD
40 MedGen
43 MeSH
44 MESH via Orphanet
45 MGI
48 NCI
49 NCIt
50 NDF-RT
52 NINDS
53 Novoseek
55 ODiseA
56 OMIM via Orphanet
57 OMIM® (Updated 24-Oct-2022)
61 PubChem
62 PubMed
64 QIAGEN
69 SNOMED-CT via HPO
70 Tocris
71 UMLS
72 UMLS via Orphanet
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