GPHYSD3
MCID: GLP007
MIFTS: 37

Geleophysic Dysplasia 3 (GPHYSD3)

Categories: Bone diseases, Fetal diseases, Genetic diseases, Rare diseases
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Aliases & Classifications for Geleophysic Dysplasia 3

MalaCards integrated aliases for Geleophysic Dysplasia 3:

Name: Geleophysic Dysplasia 3 57 11 73 28 5 14 38
Gphysd3 57 11 73

Characteristics:


Inheritance:

Autosomal dominant 57

OMIM®:

57 (Updated 08-Dec-2022)
Miscellaneous:
based on report of a family and 2 unrelated patients (last curated december 2017)
early death due to respiratory failure (in some patients)


Classifications:



Summaries for Geleophysic Dysplasia 3

UniProtKB/Swiss-Prot: 73 A form of geleophysic dysplasia, a rare skeletal disease characterized by severe short stature, short hands and feet, and joint limitations. Radiologic features include delayed bone age, cone-shaped epiphyses, shortened long tubular bones, and ovoid vertebral bodies. Affected individuals have characteristic facial features including a 'happy' face with full cheeks, shortened nose, hypertelorism, long and flat philtrum, and thin upper lip. Other distinctive features include skin thickening, progressive cardiac valvular thickening often leading to an early death, toe walking, tracheal stenosis, respiratory insufficiency, and lysosomal-like storage vacuoles in various tissues. GPHYSD3 inheritance is autosomal dominant.

MalaCards based summary: Geleophysic Dysplasia 3, also known as gphysd3, is related to hydrophthalmos and spastic paraplegia 76, autosomal recessive. An important gene associated with Geleophysic Dysplasia 3 is LTBP3 (Latent Transforming Growth Factor Beta Binding Protein 3), and among its related pathways/superpathways are Phospholipase-C Pathway and Extracellular matrix organization. Affiliated tissues include bone, skin and trachea, and related phenotypes are polyhydramnios and long philtrum

Disease Ontology: 11 A geleophysic dysplasia that has material basis in heterozygous mutation in LTBP3 on chromosome 11q13.1.

More information from OMIM: 617809 PS231050

Related Diseases for Geleophysic Dysplasia 3

Diseases in the Geleophysic Dysplasia family:

Geleophysic Dysplasia 1 Geleophysic Dysplasia 2
Geleophysic Dysplasia 3

Diseases related to Geleophysic Dysplasia 3 via text searches within MalaCards or GeneCards Suite gene sharing:

(show all 38)
# Related Disease Score Top Affiliating Genes
1 hydrophthalmos 10.1 LTBP3 LTBP2
2 spastic paraplegia 76, autosomal recessive 10.1 LTBP3 LTBP2
3 brachyolmia 10.1 LTBP3 LTBP2
4 primary congenital glaucoma 10.1 LTBP3 LTBP2
5 juvenile glaucoma 10.1 LTBP3 LTBP2
6 glaucoma 3, primary congenital, a 10.0 LTBP3 LTBP2
7 axenfeld-rieger syndrome 10.0 LTBP3 LTBP2
8 nanophthalmos 10.0 LTBP3 LTBP2
9 cutis laxa 9.9 LTBP3 FBN1
10 aniridia 1 9.9 LTBP3 LTBP2
11 weill-marchesani syndrome 1 9.9 LTBP2 FBN1
12 anterior segment dysgenesis 9.8 LTBP3 LTBP2
13 exfoliation syndrome 9.8 LTBP2 FBN1
14 cutis laxa, autosomal recessive, type ic 9.7 LTBP3 LTBP2 FBN1
15 dental anomalies and short stature 9.7 LTBP3 LTBP2 FBN1
16 autosomal recessive cutis laxa type i 9.7 LTBP3 LTBP2 FBN1
17 phacogenic glaucoma 9.7 LTBP3 LTBP2 FBN1
18 megalocornea 9.7 LTBP3 LTBP2 FBN1
19 iris disease 9.7 LTBP3 LTBP2 FBN1
20 loeys-dietz syndrome 9.7 LTBP3 LTBP2 FBN1
21 bone development disease 9.7 FBN1 ADAMTSL2
22 orthostatic intolerance 9.7 LTBP3 LTBP2 FBN1
23 glaucoma, primary open angle 9.7 LTBP3 LTBP2 FBN1
24 tracheal disease 9.6 TBRG1 FBN1 ADAMTSL2
25 brachydactyly 9.6 LTBP2 FBN1 ADAMTSL2
26 lens subluxation 9.5 LTBP3 LTBP2 FBN1 ADAMTSL2
27 contractural arachnodactyly, congenital 9.5 LTBP3 LTBP2 FBN1 ADAMTSL2
28 tracheal stenosis 9.5 TBRG1 LTBP3 FBN1 ADAMTSL2
29 peters-plus syndrome 9.4 TSR3 TSR1 LTBP3 LTBP2 ADAMTSL2
30 stiff skin syndrome 9.3 TBRG1 LTBP3 LTBP2 FBN1 ADAMTSL2
31 acromicric dysplasia 9.3 TBRG1 LTBP3 LTBP2 FBN1 ADAMTSL2
32 isolated ectopia lentis 9.3 TBRG1 LTBP3 LTBP2 FBN1 ADAMTSL2
33 weill-marchesani syndrome 9.3 TBRG1 LTBP3 LTBP2 FBN1 ADAMTSL2
34 aortic aneurysm, familial thoracic 1 9.3 TBRG1 LTBP3 LTBP2 FBN1 ADAMTSL2
35 osteochondrodysplasia 9.3 TBRG1 LTBP3 LTBP2 FBN1 ADAMTSL2
36 geleophysic dysplasia 8.7 TSR3 TSR1 TBRG1 LTBP3 LTBP2 FBN1
37 geleophysic dysplasia 2 8.7 TSR2 TSR1 TBRG1 LTBP3 LTBP2 FBN1
38 geleophysic dysplasia 1 8.5 TSR3 TSR2 TSR1 TBRG1 LTBP3 LTBP2

Graphical network of the top 20 diseases related to Geleophysic Dysplasia 3:



Diseases related to Geleophysic Dysplasia 3

Symptoms & Phenotypes for Geleophysic Dysplasia 3

Human phenotypes related to Geleophysic Dysplasia 3:

30 (show all 23)
# Description HPO Frequency Orphanet Frequency HPO Source Accession
1 polyhydramnios 30 Very rare (1%) HP:0001561
2 long philtrum 30 Very rare (1%) HP:0000343
3 sleep apnea 30 HP:0010535
4 hepatomegaly 30 HP:0002240
5 delayed skeletal maturation 30 HP:0002750
6 depressed nasal bridge 30 HP:0005280
7 wide nasal bridge 30 HP:0000431
8 thick vermilion border 30 HP:0012471
9 anteverted nares 30 HP:0000463
10 short stature 30 HP:0004322
11 epiphyseal dysplasia 30 HP:0002656
12 dyspnea 30 HP:0002094
13 brachydactyly 30 HP:0001156
14 bulbous nose 30 HP:0000414
15 hoarse voice 30 HP:0001609
16 round face 30 HP:0000311
17 respiratory failure 30 HP:0002878
18 short foot 30 HP:0001773
19 thickened skin 30 HP:0001072
20 pneumonia 30 HP:0002090
21 tracheal stenosis 30 HP:0002777
22 limb undergrowth 30 HP:0009826
23 subglottic stenosis 30 HP:0001607

Symptoms via clinical synopsis from OMIM®:

57 (Updated 08-Dec-2022)
Respiratory Nasopharynx:
sleep apnea

Head And Neck Nose:
depressed nasal bridge
anteverted nares
bulbous nose
broad nasal bridge

Respiratory:
dyspnea

Head And Neck Face:
round face
long philtrum (in some patients)

Respiratory Airways:
tracheal stenosis

Skin Nails Hair Skin:
thick skin

Muscle Soft Tissue:
pseudomuscular build

Head And Neck Mouth:
thick lips

Skeletal Feet:
short feet

Prenatal Manifestations Amniotic Fluid:
polyhydramnios (in some patients)

Abdomen Liver:
hepatomegaly

Growth Height:
short stature

Voice:
hoarse voice

Respiratory Lung:
respiratory failure
alveolointerstitial pneumonia

Respiratory Larynx:
subglottic stenosis

Cardiovascular Vascular:
pulmonary hypertension

Head And Neck Eyes:
well-defined eyebrows

Skeletal:
delayed bone age

Skeletal Limbs:
short limbs
limited movement at elbows
limited movement at wrists
epiphyseal dysplasia of proximal femur

Skeletal Hands:
marked brachydactyly
difficulty making a fist
external notch on second metacarpal
internal notch on fifth metacarpal

Clinical features from OMIM®:

617809 (Updated 08-Dec-2022)

Drugs & Therapeutics for Geleophysic Dysplasia 3

Search Clinical Trials, NIH Clinical Center for Geleophysic Dysplasia 3

Genetic Tests for Geleophysic Dysplasia 3

Genetic tests related to Geleophysic Dysplasia 3:

# Genetic test Affiliating Genes
1 Geleophysic Dysplasia 3 28 LTBP3

Anatomical Context for Geleophysic Dysplasia 3

Organs/tissues related to Geleophysic Dysplasia 3:

MalaCards : Bone, Skin, Trachea, Lung
ODiseA: Respiratory System-Trachea, Respiratory System-Lung, Respiratory System

Publications for Geleophysic Dysplasia 3

Articles related to Geleophysic Dysplasia 3:

# Title Authors PMID Year
1
Mutations in LTBP3 cause acromicric dysplasia and geleophysic dysplasia. 57 5
27068007 2016
2
Genotype-phenotype correlation and expansion of orodental anomalies in LTBP3-related disorders. 62 5
30887145 2019
3
Geleophysic dysplasia: novel missense variants and insights into ADAMTSL2 intracellular trafficking. 62
31516831 2019

Variations for Geleophysic Dysplasia 3

ClinVar genetic disease variations for Geleophysic Dysplasia 3:

5
# Gene Name Type Significance ClinVarId dbSNP ID Position
1 LTBP3 NM_001130144.3(LTBP3):c.3912A>T (p.Ter1304Cys) SNV Pathogenic
448912 rs1554971742 GRCh37: 11:65306551-65306551
GRCh38: 11:65539080-65539080
2 LTBP3 NM_001130144.3(LTBP3):c.1846+5G>A SNV Pathogenic
448913 rs1188540819 GRCh37: 11:65315386-65315386
GRCh38: 11:65547915-65547915
3 LTBP3 NM_001130144.3(LTBP3):c.2017G>T (p.Gly673Cys) SNV Pathogenic
1327506 GRCh37: 11:65315000-65315000
GRCh38: 11:65547529-65547529
4 LTBP3 NM_001130144.3(LTBP3):c.2087C>G (p.Ser696Cys) SNV Uncertain Significance
448911 rs1554974135 GRCh37: 11:65314930-65314930
GRCh38: 11:65547459-65547459
5 LTBP3 NM_001130144.3(LTBP3):c.1942C>T (p.Arg648Cys) SNV Uncertain Significance
1683537 GRCh37: 11:65315197-65315197
GRCh38: 11:65547726-65547726
6 LTBP3 NM_001130144.3(LTBP3):c.989C>T (p.Pro330Leu) SNV Uncertain Significance
548546 rs28403592 GRCh37: 11:65320709-65320709
GRCh38: 11:65553238-65553238
7 LTBP3 NM_001130144.3(LTBP3):c.1072G>A (p.Glu358Lys) SNV Not Provided
1003708 rs913431428 GRCh37: 11:65320445-65320445
GRCh38: 11:65552974-65552974
8 LTBP3 NM_001130144.3(LTBP3):c.2893+1G>T SNV Not Provided
1067470 GRCh37: 11:65308596-65308596
GRCh38: 11:65541125-65541125
9 LTBP3 NM_001130144.3(LTBP3):c.76CTG[9] (p.Leu35del) MICROSAT Not Provided
532697 rs71036212 GRCh37: 11:65325326-65325328
GRCh38: 11:65557855-65557857

Expression for Geleophysic Dysplasia 3

Search GEO for disease gene expression data for Geleophysic Dysplasia 3.

Pathways for Geleophysic Dysplasia 3

Pathways related to Geleophysic Dysplasia 3 according to GeneCards Suite gene sharing:

(show all 12)
# Super pathways Score Top Affiliating Genes
1
Show member pathways
12.56 TBRG1 LTBP3 LTBP2 FBN1
2
Show member pathways
12.3 LTBP3 LTBP2 FBN1
3
Show member pathways
12.25 TBRG1 LTBP3 LTBP2
4
Show member pathways
12.19 TBRG1 LTBP3 LTBP2
5
Show member pathways
11.98 LTBP3 LTBP2 FBN1
6
Show member pathways
11.96 TBRG1 LTBP3 LTBP2
7
Show member pathways
11.39 LTBP3 FBN1 ADAMTSL2
8 11.3 TBRG1 LTBP3 LTBP2
9
Show member pathways
11.13 LTBP3 LTBP2 FBN1
10 10.72 LTBP2 FBN1
11
Show member pathways
10.71 LTBP3 LTBP2 FBN1
12 10.46 TBRG1 LTBP3 LTBP2 FBN1

GO Terms for Geleophysic Dysplasia 3

Cellular components related to Geleophysic Dysplasia 3 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 extracellular matrix GO:0031012 9.17 LTBP3 LTBP2 FBN1 ADAMTSL2

Biological processes related to Geleophysic Dysplasia 3 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) GO:0000462 8.92 TSR2 TSR1

Molecular functions related to Geleophysic Dysplasia 3 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 growth factor binding GO:0019838 9.13 LTBP3 LTBP2
2 microfibril binding GO:0050436 8.92 LTBP2 ADAMTSL2

Sources for Geleophysic Dysplasia 3

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 08-Dec-2022)
61 PubChem
62 PubMed
64 QIAGEN
69 SNOMED-CT via HPO
70 Tocris
71 UMLS
72 UMLS via Orphanet
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