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SCDO3
MCID: SPN297
MIFTS: 54

Spondylocostal Dysostosis 3, Autosomal Recessive (SCDO3)

Categories: Bone diseases, Fetal diseases, Genetic diseases, Metabolic diseases, Neuronal diseases, Rare diseases, Respiratory diseases
Genes Variations Tissues Related diseases Publications Pathways Symptoms & Phenotypes
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Aliases & Classifications for Spondylocostal Dysostosis 3, Autosomal Recessive

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MalaCards integrated aliases for Spondylocostal Dysostosis 3, Autosomal Recessive:

Name: Spondylocostal Dysostosis 3, Autosomal Recessive 57 20 72 29 6
Spondylocostal Dysostosis 12 20 43 36 6 15
Spondylocostal Dysostosis, Autosomal Recessive 3 12 13 70
Jarcho-Levin Syndrome 12 43 70
Scdo3 57 72
Scdo 20 43
Dysostosis, Spondylocostal, Autosomal Recessive, Type 3 39
Spondylothoracic Dysostosis 12
Spondylocostal Dysostosis 3 20
Spondylothoracic Dysplasia 12
Dysostosis, Spondylocostal 39
Costovertebral Dysplasia 20
Scod3 20

Characteristics:

OMIM®:

57 (Updated 20-May-2021)
Inheritance:
autosomal recessive

Miscellaneous:
two patients have been independently reported (last curated february 2019)


HPO:

31
spondylocostal dysostosis 3, autosomal recessive:
Inheritance autosomal recessive inheritance


Classifications:

MalaCards categories:
Global: Genetic diseases Rare diseases Metabolic diseases Fetal diseases
Anatomical: Bone diseases Neuronal diseases Respiratory diseases
See all MalaCards categories (disease lists)


External Ids:

Disease Ontology 12 DOID:0050568
OMIM® 57 609813
OMIM Phenotypic Series 57 PS277300
KEGG 36 H00517
MeSH 44 D004413
MedGen 41 C1853296
UMLS 70 C0265343 C1853296
Sources

Summaries for Spondylocostal Dysostosis 3, Autosomal Recessive

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MedlinePlus Genetics : 43 Spondylocostal dysostosis is a group of conditions characterized by abnormal development of bones in the spine and ribs. The bones of the spine (vertebrae) are misshapen and abnormally joined together (fused). Many people with this condition have abnormal side-to-side curvature of the spine (scoliosis) due to malformation of the vertebrae. In addition to spinal abnormalities, some of the rib bones may be fused together or missing. Affected individuals have short, rigid necks and short torsos because of the bone malformations. As a result, people with spondylocostal dysostosis have short bodies but normal-length arms and legs, called short-trunk dwarfism.The spine and rib abnormalities, which are present from birth, cause other signs and symptoms of spondylocostal dysostosis. Infants with this condition have small chests that cannot expand adequately, often leading to life-threatening breathing problems. As the lungs expand in the narrow chest, the muscle that separates the abdomen from the chest cavity (the diaphragm) is forced down and the abdomen is pushed out. The increased pressure in the abdomen can cause a soft out-pouching around the lower abdomen (inguinal hernia), particularly in males with spondylocostal dysostosis.Some people with spondylocostal dysostosis also have a type of birth defect known as a neural tube defect. Neural tube defects occur when a structure called the neural tube, a layer of cells that ultimately develops into the brain and spinal cord, fails to close completely during the first few weeks of embryonic development. Examples of neural tube defects that occur in people with spondylocostal dysostosis include a spinal cord abnormality known as spina bifida and a brain abnormality called a Chiari malformation.Although breathing problems can be fatal early in life, many affected individuals live into adulthood.Spondylocostal dysostosis has often been grouped with a similar condition called spondylothoracic dysostosis, and both are sometimes called Jarcho-Levin syndrome; however, they are now considered distinct conditions.

MalaCards based summary : Spondylocostal Dysostosis 3, Autosomal Recessive, also known as spondylocostal dysostosis, is related to spondylocostal dysostosis 5 and spondylocostal dysostosis 1, autosomal recessive. An important gene associated with Spondylocostal Dysostosis 3, Autosomal Recessive is LFNG (LFNG O-Fucosylpeptide 3-Beta-N-Acetylglucosaminyltransferase), and among its related pathways/superpathways are Notch signaling pathway and PI3K-Akt signaling pathway. Affiliated tissues include vertebrae, ribs and spinal cord, and related phenotypes are scoliosis and kyphosis

Disease Ontology : 12 A dysostosis that results in abnormal development located in vertebrae or located in ribs. The bones of the spine do not develop properly, which causes them to be misshapen and abnormally joined together.

GARD : 20 Spondylocostal dysostosis is a group of conditions characterized by abnormal development of the bones in the spine and ribs. In the spine, the vertebrae are misshapen and fused. Many people with this condition have an abnormal side-to-side curvature of the spine ( scoliosis ). The ribs may be fused together or missing. These bone malformations lead to short, rigid necks and short midsections. Infants with spondylocostal dysostosis have small, narrow chests that cannot fully expand. This can lead to life-threatening breathing problems. Males with this condition are at an increased risk for inguinal hernia, where the diaphragm is pushed down, causing the abdomen to bulge out. There are several types of spondylocostal dysostosis. These types have similar features and are distinguished by their genetic cause and how they are inherited, autosomal recessive or autosomal dominant. Some of the autosomal recessive types of spondylocostal dysostosis are called "Jarcho-Levin syndrome ", a term that is more often used as a synonym for a similar condition known as " spondylothoracic dysostosis ". Treatment is symptomatic and supportive and may include respiratory support and surgery to correct inguinal hernia and scoliosis.

KEGG : 36 Spondylocostal dysostosis (SCDO) is a group of disorders characterized by vertebral defects along the entire spinal column with rib fusions and deletions. SCD arises from disturbed somite segmentation during embryonic development due to mutations in Notch pathway genes.

UniProtKB/Swiss-Prot : 72 Spondylocostal dysostosis 3, autosomal recessive: A condition of variable severity associated with vertebral and rib segmentation defects. The main skeletal malformations include fusion of vertebrae, hemivertebrae, fusion of certain ribs, and other rib malformations. Deformity of the chest and spine (severe scoliosis, kyphoscoliosis and lordosis) is a natural consequence of the malformation and leads to a dwarf-like appearance. As the thorax is small, infants frequently have respiratory insufficiency and repeated respiratory infections resulting in life-threatening complications in the first year of life.

Wikipedia : 73 Spondylocostal dysostosis, also known as Jarcho-Levin syndrome (JLS), is a rare, heritable axial... more...

More information from OMIM: 609813 PS277300
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Related Diseases for Spondylocostal Dysostosis 3, Autosomal Recessive

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Diseases in the Spondylocostal Dysostosis, Autosomal Recessive family:

Spondylocostal Dysostosis 5 Spondylocostal Dysostosis 1, Autosomal Recessive
Spondylocostal Dysostosis 2, Autosomal Recessive Spondylocostal Dysostosis 3, Autosomal Recessive
Spondylocostal Dysostosis 4, Autosomal Recessive Spondylocostal Dysostosis 6, Autosomal Recessive

Diseases related to Spondylocostal Dysostosis 3, Autosomal Recessive via text searches within MalaCards or GeneCards Suite gene sharing:

(show top 50) (show all 102)
# Related Disease Score Top Affiliating Genes
1 spondylocostal dysostosis 5 33.0 TBX6 MESP2 HES7
2 spondylocostal dysostosis 1, autosomal recessive 32.2 MESP2 LFNG HES7 DLL3
3 meningocele 30.6 MESP2 HES7
4 spina bifida occulta 30.6 MESP2 HES7
5 dysostosis 30.6 TBX6 RIPPLY2 MESP2 LFNG HES7 DLL3
6 spondylocostal dysostosis, autosomal recessive 30.2 TBX6 RIPPLY2 MESP2 LFNG HES7 DLL3
7 scoliosis 30.1 TBX6 RIPPLY2 MESP2 LFNG JAG1 HES7
8 tetralogy of fallot 29.5 RBPJ NOTCH2 NOTCH1 JAG1
9 spondylocostal dysostosis 6, autosomal recessive 11.8
10 spondylocostal dysostosis 4, autosomal recessive 11.7
11 hydrocephalus, sprengel anomaly, and costovertebral dysplasia 11.6
12 spondylocostal dysostosis-hypospadias-intellectual disability syndrome 11.1
13 neural tube defects 10.7
14 hydrocephalus 10.4
15 respiratory failure 10.4
16 diastematomyelia 10.4
17 osteochondrodysplasia 10.3
18 vesicoureteral reflux 1 10.3
19 chiari malformation type ii 10.3
20 chiari malformation 10.3
21 anus, imperforate 10.3
22 gallbladder benign neoplasm 10.2 SRRT LFNG
23 meckel diverticulum 10.1
24 osteoporosis 10.1
25 pancreas, annular 10.1
26 syringomyelia, noncommunicating isolated 10.1
27 duodenal atresia 10.1
28 bone mineral density quantitative trait locus 8 10.1
29 bone mineral density quantitative trait locus 15 10.1
30 pulmonary hypertension 10.1
31 myelomeningocele 10.1
32 intestinal atresia 10.1
33 placenta praevia 10.1
34 synostosis 10.1
35 hypothyroidism 10.1
36 heart septal defect 10.1
37 atrial heart septal defect 10.1
38 glomus tumor 10.1
39 syringomyelia 10.1
40 holoprosencephaly 10.1
41 polyhydramnios 10.1
42 back pain 10.1
43 overgrowth syndrome 10.1
44 bone structure disease 10.1 TBX6 MESP2 HES7
45 lacrimal gland adenoid cystic carcinoma 10.1 NOTCH2 NOTCH1
46 diaphragmatic hernia, congenital 10.1
47 robinow syndrome, autosomal recessive 1 10.1
48 spondylocostal dysostosis with anal atresia and urogenital anomalies 10.1
49 spondylocostal dysostosis 2, autosomal recessive 10.1
50 helix syndrome 10.1

Graphical network of the top 20 diseases related to Spondylocostal Dysostosis 3, Autosomal Recessive:



Diseases related to Spondylocostal Dysostosis 3, Autosomal Recessive
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Symptoms & Phenotypes for Spondylocostal Dysostosis 3, Autosomal Recessive

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Human phenotypes related to Spondylocostal Dysostosis 3, Autosomal Recessive:

31 (show all 8)
# Description HPO Frequency HPO Source Accession
1 scoliosis 31 HP:0002650
2 kyphosis 31 HP:0002808
3 short stature 31 HP:0004322
4 vertebral segmentation defect 31 HP:0003422
5 rib fusion 31 HP:0000902
6 hypoplasia of the odontoid process 31 HP:0003311
7 slender finger 31 HP:0001238
8 supernumerary vertebral ossification centers 31 HP:0004598

Symptoms via clinical synopsis from OMIM®:

57 (Updated 20-May-2021)
Skeletal Spine:
kyphosis
hypoplastic odontoid process
multiple vertebral anomalies
'pebble-beach' appearance of vertebral bodies
multiple vertebral ossification centers
more
Chest Ribs Sternum Clavicles And Scapulae:
fused ribs

Skeletal Limbs:
normal long bones

Growth Height:
short stature

Skeletal Pelvis:
normal pelvis

Clinical features from OMIM®:

609813 (Updated 20-May-2021)

MGI Mouse Phenotypes related to Spondylocostal Dysostosis 3, Autosomal Recessive:

46 (show all 11)
# Description MGI Source Accession Score Top Affiliating Genes
1 embryo MP:0005380 10.36 DLL1 DLL3 HES7 JAG1 LFNG MESP2
2 growth/size/body region MP:0005378 10.25 DLL1 DLL3 HES7 JAG1 LFNG MESP2
3 mortality/aging MP:0010768 10.25 DLL1 DLL3 EOGT HES7 JAG1 LFNG
4 cardiovascular system MP:0005385 10.19 DLL1 JAG1 LFNG MESP2 NOTCH1 NOTCH2
5 endocrine/exocrine gland MP:0005379 10.13 DLL1 JAG1 LFNG MFNG NOTCH1 NOTCH2
6 limbs/digits/tail MP:0005371 10.11 DLL1 DLL3 HES7 LFNG MESP2 MFNG
7 digestive/alimentary MP:0005381 10.02 DLL1 JAG1 NOTCH1 NOTCH2 RBPJ RFNG
8 muscle MP:0005369 9.91 DLL1 DLL3 JAG1 MESP2 NOTCH1 NOTCH2
9 nervous system MP:0003631 9.9 DLL1 DLL3 JAG1 LFNG MESP2 NOTCH1
10 normal MP:0002873 9.56 DLL1 JAG1 MESP2 MFNG NOTCH1 NOTCH2
11 skeleton MP:0005390 9.47 DLL1 DLL3 HES7 JAG1 LFNG MESP2
Sources

Drugs & Therapeutics for Spondylocostal Dysostosis 3, Autosomal Recessive

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Search Clinical Trials , NIH Clinical Center for Spondylocostal Dysostosis 3, Autosomal Recessive

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Genetic Tests for Spondylocostal Dysostosis 3, Autosomal Recessive

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Genetic tests related to Spondylocostal Dysostosis 3, Autosomal Recessive:

# Genetic test Affiliating Genes
1 Spondylocostal Dysostosis 3, Autosomal Recessive 29 LFNG
Sources

Anatomical Context for Spondylocostal Dysostosis 3, Autosomal Recessive

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The Foundational Model of Anatomy Ontology organs/tissues related to Spondylocostal Dysostosis 3, Autosomal Recessive:

19
Vertebrae, Ribs

MalaCards organs/tissues related to Spondylocostal Dysostosis 3, Autosomal Recessive:

40
Spinal Cord, Bone, Heart, Spleen, Lung, Pancreas, Placenta
Sources

Publications for Spondylocostal Dysostosis 3, Autosomal Recessive

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Articles related to Spondylocostal Dysostosis 3, Autosomal Recessive:

(show top 50) (show all 163)
# Title Authors PMID Year
1
Identification of novel LFNG mutations in spondylocostal dysostosis. 57 6 61
30531807 2019
2
Mutation of the LUNATIC FRINGE gene in humans causes spondylocostal dysostosis with a severe vertebral phenotype. 61 6 57
16385447 2006
3
Mutated MESP2 causes spondylocostal dysostosis in humans. 57 61
15122512 2004
4
Congenital cervical spine malformation due to bi-allelic RIPPLY2 variants in spondylocostal dysostosis type 6. 61
33410135 2021
5
Clinical and molecular delineation of spondylocostal dysostosis type 3. 61
33728697 2021
6
Altered Cogs of the Clock: Insights into the Embryonic Etiology of Spondylocostal Dysostosis. 61
33572886 2021
7
Diseases related to Notch glycosylation. 61
33341260 2020
8
An additional piece in the TBX6 gene dosage model: A novel nonsense variant in a fetus with severe spondylocostal dysostosis. 61
33058178 2020
9
High-flow nasal cannula therapy in a case of spondylocostal dysostosis type 2. 61
33089894 2020
10
Congenital posterior cervical spine malformation due to biallelic c.240-4T>G RIPPLY2 variant: A discrete entity. 61
32212228 2020
11
Recapitulating the human segmentation clock with pluripotent stem cells. 61
32238941 2020
12
Retrospective analysis of fetal vertebral defects: Associated anomalies, etiologies, and outcome. 61
31880412 2020
13
Jarcho-Levin Syndrome: Two Consecutive Cases in the Same Family. 61
32518573 2019
14
Butterfly Vertebrae: A Systematic Review of the Literature and Analysis. 61
31448202 2019
15
Bi-allelic loss of function variants of TBX6 causes a spectrum of malformation of spine and rib including congenital scoliosis and spondylocostal dysostosis. 61
31015262 2019
16
An In Vitro Human Segmentation Clock Model Derived from Embryonic Stem Cells. 61
31461642 2019
17
Phenotypic heterogeneity of kyphoscoliosis with vertebral and rib defects: a case series. 61
30921094 2019
18
Spondylocostal Dysostosis (Jarcho-Levin Syndrome) in an Adult Patient with Consanguineous Parents, in Long-Term Follow-Up. 61
30448585 2019
19
Spondylocostal Dysostosis Associated with Split Spinal Cord and Other Malformations. 61
31597143 2019
20
A Cryptic Cause of Cardiac Arrest. 61
30420309 2019
21
Screening of known disease genes in congenital scoliosis. 61
30196550 2018
22
Diagnostic strategy in segmentation defect of the vertebrae: a retrospective study of 73 patients. 61
29459493 2018
23
Spondylocostal Dysostosis (Jarcho Levin Syndrome). 61
29270795 2018
24
Homozygous DMRT2 variant associates with severe rib malformations in a newborn. 61
29681102 2018
25
Spondylocostal Dysostosis: A Literature Review and Case Report with Long-Term Follow-Up of a Conservatively Managed Patient. 61
29765785 2018
26
Response to Lefebvre et al. 61
28990171 2017
27
Lipomeningomyelocele with Fatty Filum Terminale in a Patient with Jarcho-Levin Syndrome: A Rare Association Requiring Special Attention. 61
29675085 2017
28
Autosomal recessive variations of TBX6, from congenital scoliosis to spondylocostal dysostosis. 61
27861764 2017
29
The developmental biology of genetic Notch disorders. 61
28512196 2017
30
Compound Heterozygosity for Null Mutations and a Common Hypomorphic Risk Haplotype in TBX6 Causes Congenital Scoliosis. 61
28054739 2017
31
Combined use of Neurally Adjusted Ventilatory Assist (NAVA) and Vertical Expandable Prostethic Titanium Rib (VEPTR) in a patient with Spondylocostal dysostosis and associated bronchomalacia. 61
28196820 2017
32
Congenital hemangioma in spondylocostal dysostosis: a novel association. 61
28300884 2016
33
Mind the gap: an unusual case of a cervical lipomyelocele. 61
27594964 2016
34
[Spondylocostal dysostosis and acute cholangitis in pediatrics emergency room]. 61
29421389 2016
35
Fetus with Casamassima-Morton-Nance Syndrome and Limb-Body Wall Defect: Presentation of a Novel Association and Review of the Phenotype. 61
26367183 2016
36
Context-Dependent Sensitivity to Mutations Disrupting the Structural Integrity of Individual EGF Repeats in the Mouse Notch Ligand DLL1. 61
26801181 2016
37
The many roles of Notch signaling during vertebrate somitogenesis. 61
25483003 2016
38
Spondylocostal dysostosis associated with right-sided polythelia, right-sided rib deformity and meningocoele: Case report with review of literature. 61
26962344 2015
39
Spondylocostal dysostosis (Jarcho-Levine syndrome) associated with occult spinal dysraphism: Report of two cases. 61
26167215 2015
40
Novel ENU-Induced Mutation in Tbx6 Causes Dominant Spondylocostal Dysostosis-Like Vertebral Malformations in the Rat. 61
26090680 2015
41
Correction: Novel ENU-Induced Mutation in Tbx6 Causes Dominant Spondylocostal Dysostosis-Like Vertebral Malformations in the Rat. 61
26222705 2015
42
Expanding the phenotype of spondylospinal thoracic dysostosis (the Turkel-Chen-Johnson syndrome). 61
25304117 2015
43
Canine disorder mirrors human disease: exonic deletion in HES7 causes autosomal recessive spondylocostal dysostosis in miniature Schnauzer dogs. 61
25659135 2015
44
Management of thoracic insufficiency syndrome in patients with Jarcho-Levin syndrome using VEPTRs (vertical expandable prosthetic titanium ribs). 61
25378514 2014
45
Spinal and pelvic corrections in a patient with spondylocostal dysplasia syndrome and hemimyelomeningocele. 61
25323186 2014
46
Spondylocostal dysostosis with lipomyelomeningocele: Case report and review of the literature. 61
25624929 2014
47
Spondylocostal dysostosis with tetralogy of Fallot and herniation of the spleen through the diaphragm. 61
24666313 2014
48
Mutation of HES7 in a large extended family with spondylocostal dysostosis and dextrocardia with situs inversus. 61
23897666 2013
49
Notch signaling in skeletal health and disease. 61
23554451 2013
50
Autosomal dominant spondylocostal dysostosis is caused by mutation in TBX6. 61
23335591 2013
Sources

Variations for Spondylocostal Dysostosis 3, Autosomal Recessive

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ClinVar genetic disease variations for Spondylocostal Dysostosis 3, Autosomal Recessive:

6 (show all 41)
# Gene Name Type Significance ClinVarId dbSNP ID Position
1 LFNG NM_001040167.2(LFNG):c.564C>A (p.Phe188Leu) SNV Pathogenic 6999 rs104894024 GRCh37: 7:2564935-2564935
GRCh38: 7:2525301-2525301
2 LFNG NM_001040167.2(LFNG):c.601G>A (p.Asp201Asn) SNV Pathogenic 619139 rs1211456697 GRCh37: 7:2565067-2565067
GRCh38: 7:2525433-2525433
3 LFNG NM_001040167.2(LFNG):c.372del (p.Lys124fs) Deletion Pathogenic 619140 rs1562551396 GRCh37: 7:2559867-2559867
GRCh38: 7:2520233-2520233
4 LFNG NM_001040167.2(LFNG):c.1013A>T (p.Glu338Val) SNV Uncertain significance 661901 rs770620949 GRCh37: 7:2566495-2566495
GRCh38: 7:2526861-2526861
5 LFNG NM_001040167.2(LFNG):c.715C>T (p.Arg239Trp) SNV Uncertain significance 665982 rs143479850 GRCh37: 7:2565181-2565181
GRCh38: 7:2525547-2525547
6 MESP2 NM_001039958.2(MESP2):c.*132_*134dup Duplication Uncertain significance 317398 rs3840032 GRCh37: 15:90321695-90321696
GRCh38: 15:89778464-89778465
7 DLL3 NM_203486.3(DLL3):c.-12dup Duplication Uncertain significance 329230 rs747003629 GRCh37: 19:39989596-39989597
GRCh38: 19:39498956-39498957
8 LFNG NM_001040167.2(LFNG):c.643G>A (p.Ala215Thr) SNV Uncertain significance 465827 rs1160316709 GRCh37: 7:2565109-2565109
GRCh38: 7:2525475-2525475
9 LFNG NM_001040167.2(LFNG):c.1003G>A (p.Gly335Ser) SNV Uncertain significance 948628 GRCh37: 7:2566485-2566485
GRCh38: 7:2526851-2526851
10 LFNG NM_001040167.2(LFNG):c.1021C>T (p.Arg341Trp) SNV Uncertain significance 971848 GRCh37: 7:2566503-2566503
GRCh38: 7:2526869-2526869
11 LFNG NM_001040167.2(LFNG):c.527C>T (p.Ala176Val) SNV Uncertain significance 982785 GRCh37: 7:2564898-2564898
GRCh38: 7:2525264-2525264
12 LFNG NM_001040167.2(LFNG):c.766G>A (p.Gly256Ser) SNV Uncertain significance 1003507 GRCh37: 7:2565349-2565349
GRCh38: 7:2525715-2525715
13 LFNG NM_001040167.2(LFNG):c.197_198delinsTT (p.Ala66Val) Indel Uncertain significance 591285 rs1562551243 GRCh37: 7:2559692-2559693
GRCh38: 7:2520058-2520059
14 LFNG NM_001040167.2(LFNG):c.307C>G (p.Pro103Ala) SNV Uncertain significance 1018847 GRCh37: 7:2559802-2559802
GRCh38: 7:2520168-2520168
15 LFNG NM_001040167.2(LFNG):c.557A>G (p.Asp186Gly) SNV Uncertain significance 1035758 GRCh37: 7:2564928-2564928
GRCh38: 7:2525294-2525294
16 LFNG NM_001040167.2(LFNG):c.295G>A (p.Ala99Thr) SNV Uncertain significance 1037213 GRCh37: 7:2559790-2559790
GRCh38: 7:2520156-2520156
17 LFNG NM_001040167.2(LFNG):c.37C>G (p.Leu13Val) SNV Uncertain significance 1038450 GRCh37: 7:2559532-2559532
GRCh38: 7:2519898-2519898
18 LFNG NM_001040167.2(LFNG):c.100C>A (p.Pro34Thr) SNV Uncertain significance 1040157 GRCh37: 7:2559595-2559595
GRCh38: 7:2519961-2519961
19 LFNG NM_001040167.2(LFNG):c.842C>T (p.Thr281Met) SNV Uncertain significance 1040378 GRCh37: 7:2565898-2565898
GRCh38: 7:2526264-2526264
20 LFNG NM_001040167.2(LFNG):c.131G>T (p.Ser44Ile) SNV Uncertain significance 1045090 GRCh37: 7:2559626-2559626
GRCh38: 7:2519992-2519992
21 LFNG NM_001040167.2(LFNG):c.308C>T (p.Pro103Leu) SNV Uncertain significance 1057386 GRCh37: 7:2559803-2559803
GRCh38: 7:2520169-2520169
22 LFNG NM_001040167.2(LFNG):c.1124G>A (p.Arg375His) SNV Uncertain significance 1059562 GRCh37: 7:2566830-2566830
GRCh38: 7:2527196-2527196
23 LFNG NM_001040167.2(LFNG):c.521G>A (p.Arg174His) SNV Uncertain significance 1062453 GRCh37: 7:2564892-2564892
GRCh38: 7:2525258-2525258
24 LFNG NM_001040167.2(LFNG):c.788G>A (p.Arg263His) SNV Uncertain significance 1063078 GRCh37: 7:2565371-2565371
GRCh38: 7:2525737-2525737
25 LFNG NM_001040167.2(LFNG):c.559C>T (p.Arg187Cys) SNV Uncertain significance 1064285 GRCh37: 7:2564930-2564930
GRCh38: 7:2525296-2525296
26 LFNG NM_001040167.2(LFNG):c.266G>T (p.Gly89Val) SNV Uncertain significance 850063 GRCh37: 7:2559761-2559761
GRCh38: 7:2520127-2520127
27 LFNG NM_001040167.2(LFNG):c.573C>T (p.Ser191=) SNV Likely benign 286065 rs139864844 GRCh37: 7:2564944-2564944
GRCh38: 7:2525310-2525310
28 LFNG NM_001040167.2(LFNG):c.735+9C>T SNV Likely benign 497705 rs202171160 GRCh37: 7:2565210-2565210
GRCh38: 7:2525576-2525576
29 LFNG NM_001040167.2(LFNG):c.653C>T (p.Pro218Leu) SNV Likely benign 465828 rs148460430 GRCh37: 7:2565119-2565119
GRCh38: 7:2525485-2525485
30 LFNG NM_001040167.2(LFNG):c.768C>T (p.Gly256=) SNV Likely benign 727402 rs113634524 GRCh37: 7:2565351-2565351
GRCh38: 7:2525717-2525717
31 LFNG NM_001040167.2(LFNG):c.6C>A (p.Leu2=) SNV Likely benign 731865 rs1390203183 GRCh37: 7:2559501-2559501
GRCh38: 7:2519867-2519867
32 LFNG NM_001040167.2(LFNG):c.582-10T>C SNV Likely benign 733999 rs1249078709 GRCh37: 7:2565038-2565038
GRCh38: 7:2525404-2525404
33 LFNG NM_001040167.2(LFNG):c.1036G>A (p.Val346Met) SNV Likely benign 786075 rs71647813 GRCh37: 7:2566518-2566518
GRCh38: 7:2526884-2526884
34 LFNG NM_001040167.2(LFNG):c.667G>A (p.Val223Ile) SNV Likely benign 800232 rs142596712 GRCh37: 7:2565133-2565133
GRCh38: 7:2525499-2525499
35 MESP2 NM_001039958.2(MESP2):c.-11G>A SNV Likely benign 257238 rs139599055 GRCh37: 15:90319578-90319578
GRCh38: 15:89776347-89776347
36 MESP2 NM_001039958.2(MESP2):c.*431C>T SNV Benign 369104 rs11073889 GRCh37: 15:90321996-90321996
GRCh38: 15:89778765-89778765
37 LFNG NM_001040167.2(LFNG):c.1104G>A (p.Pro368=) SNV Benign 715354 rs544123371 GRCh37: 7:2566810-2566810
GRCh38: 7:2527176-2527176
38 LFNG NM_001040167.2(LFNG):c.481+3G>A SNV Benign 257265 rs141008352 GRCh37: 7:2564380-2564380
GRCh38: 7:2524746-2524746
39 LFNG NM_001040167.2(LFNG):c.920G>A (p.Arg307His) SNV Benign 728667 rs201791522 GRCh37: 7:2565976-2565976
GRCh38: 7:2526342-2526342
40 LFNG NM_001040167.2(LFNG):c.482-4A>G SNV Benign 257266 rs62444250 GRCh37: 7:2564849-2564849
GRCh38: 7:2525215-2525215
41 MESP2 NM_001039958.2(MESP2):c.552_557GGGGCA[1] (p.180_181QG[11]) Microsatellite Benign 281200 rs56192595 GRCh37: 15:90320135-90320146
GRCh38: 15:89776904-89776915

UniProtKB/Swiss-Prot genetic disease variations for Spondylocostal Dysostosis 3, Autosomal Recessive:

72
# Symbol AA change Variation ID SNP ID
1 LFNG p.Phe188Leu VAR_025850 rs104894024

Copy number variations for Spondylocostal Dysostosis 3, Autosomal Recessive from CNVD:

7
# CNVD ID Chromosome Start End Type Gene Symbol CNVD Disease
1 96229 15 86900000 92100000 Copy number MESP2 Spondylocostal dysostosis
2 116536 17 6800000 11200000 Copy number HES7 Spondylocostal dysostosis
3 128868 19 43400000 47800000 Copy number DLL3 Spondylocostal dysostosis
4 223467 7 2100000 4500000 Copy number LFNG Spondylocostal dysostosis
Sources

Expression for Spondylocostal Dysostosis 3, Autosomal Recessive

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Search GEO for disease gene expression data for Spondylocostal Dysostosis 3, Autosomal Recessive.
Sources

Pathways for Spondylocostal Dysostosis 3, Autosomal Recessive

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Pathways related to Spondylocostal Dysostosis 3, Autosomal Recessive according to KEGG:

36
# Name Kegg Source Accession
1 Notch signaling pathway hsa04330

Pathways related to Spondylocostal Dysostosis 3, Autosomal Recessive according to GeneCards Suite gene sharing:

(show all 24)
# Super pathways Score Top Affiliating Genes
1
PI3K-Akt signaling pathway 36
Show member pathways
 12.96 RFNG RBPJ NOTCH2 NOTCH1 MFNG LFNG
2
Signaling by NOTCH1 65
Show member pathways
 12.84 RFNG RBPJ POGLUT1 POFUT1 NOTCH2 NOTCH1
3
Pathways in cancer 36
12.71 NOTCH2 NOTCH1 JAG1 DLL3 DLL1
4
Gastric cancer 36
Show member pathways
 12.65 NOTCH2 NOTCH1 JAG1 DLL3 DLL1
5
Glioma 36
Show member pathways
 12.58 NOTCH2 NOTCH1 JAG1 DLL3 DLL1
6
Th17 cell differentiation 36
Show member pathways
 12.56 RBPJ NOTCH2 NOTCH1 JAG1 DLL3 DLL1
7
Mesodermal Commitment Pathway 1
Show member pathways
 12.39 TBX6 NOTCH1 HES7 DLL1
8
Notch Signaling Pathway (WikiPathways) 36
Show member pathways
 12.37 RFNG RBPJ POFUT1 NOTCH2 NOTCH1 MFNG
9
Wnt / Hedgehog / Notch 4
12.26 RBPJ NOTCH2 NOTCH1 LFNG JAG1 DLL3
10
Development NOTCH1-mediated pathway for NF-KB activity modulation 23
Show member pathways
 12.21 RFNG RBPJ NOTCH1 MFNG LFNG JAG1
11
NOTCH2 Activation and Transmission of Signal to the Nucleus 65
Show member pathways
 12.09 RBPJ NOTCH2 NOTCH1 JAG1 DLL1
12
Mucin type O-glycan biosynthesis 36
Show member pathways
 11.99 RFNG POGLUT1 POFUT1 MFNG LFNG EOGT
13
Neural Crest Differentiation 1
11.96 TBX6 RBPJ NOTCH2 NOTCH1 DLL3 DLL1
14
Pre-NOTCH Expression and Processing 65
Show member pathways
 11.96 RFNG RBPJ POGLUT1 POFUT1 NOTCH2 NOTCH1
15
Presenilin-Mediated Signaling 63
11.95 RBPJ NOTCH2 NOTCH1
16
Angiogenesis (CST) 4
11.72 NOTCH2 NOTCH1 JAG1
17
Th2 Differentiation Pathway 64
11.41 RBPJ NOTCH1 JAG1
18
Presenilin action in Notch and Wnt signaling 1
11.4 RBPJ NOTCH1 DLL1
19
Notch Signaling 63
11.32 RFNG RBPJ NOTCH2 NOTCH1 MFNG LFNG
20
Canonical and Non-canonical Notch signaling 1
11.23 RBPJ NOTCH2 NOTCH1 JAG1 DLL3 DLL1
21
Notch Signaling Pathway (sino) 66
11.1 RFNG RBPJ POFUT1 NOTCH2 NOTCH1 MFNG
22
NOTCH1 regulation of human endothelial cell calcification 1
11.07 NOTCH1 JAG1 DLL3 DLL1
23
Amplification and Expansion of Oncogenic Pathways as Metastatic Traits 1
10.84 NOTCH1 JAG1
24
Gene regulatory network modelling somitogenesis 1
10.54 TBX6 RIPPLY2 NOTCH1 MESP2 LFNG HES7
Sources

GO Terms for Spondylocostal Dysostosis 3, Autosomal Recessive

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Cellular components related to Spondylocostal Dysostosis 3, Autosomal Recessive according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 Golgi membrane GO:0000139 9.55 RFNG NOTCH2 NOTCH1 MFNG LFNG
2 integral component of Golgi membrane GO:0030173 9.13 RFNG MFNG LFNG
3 MAML1-RBP-Jkappa- ICN1 complex GO:0002193 8.62 RBPJ NOTCH1

Biological processes related to Spondylocostal Dysostosis 3, Autosomal Recessive according to GeneCards Suite gene sharing:

(show top 50) (show all 60)
# Name GO ID Score Top Affiliating Genes
1 regulation of transcription, DNA-templated GO:0006355 10.24 TBX6 SRRT RBPJ POFUT1 NOTCH2 NOTCH1
2 negative regulation of transcription by RNA polymerase II GO:0000122 10.17 TBX6 RIPPLY2 RBPJ NOTCH2 NOTCH1 HES7
3 multicellular organism development GO:0007275 10.13 TBX6 RIPPLY2 RFNG POGLUT1 NOTCH2 NOTCH1
4 positive regulation of cell proliferation GO:0008284 10.1 TBX6 RBPJ NOTCH2 NOTCH1 DLL1
5 angiogenesis GO:0001525 10 RBPJ POFUT1 NOTCH1 JAG1
6 animal organ morphogenesis GO:0009887 9.97 RFNG NOTCH2 LFNG JAG1
7 determination of left/right symmetry GO:0007368 9.87 RIPPLY2 NOTCH2 NOTCH1 DLL1
8 negative regulation of neuron differentiation GO:0045665 9.86 NOTCH1 JAG1 DLL1
9 keratinocyte differentiation GO:0030216 9.86 RBPJ NOTCH1 JAG1
10 humoral immune response GO:0006959 9.85 RBPJ NOTCH2 NOTCH1
11 pattern specification process GO:0007389 9.85 RFNG MFNG LFNG
12 hemopoiesis GO:0030097 9.85 RBPJ NOTCH2 JAG1 DLL1
13 heart looping GO:0001947 9.84 TBX6 NOTCH2 NOTCH1 DLL1
14 regulation of neurogenesis GO:0050767 9.82 NOTCH1 HES7 DLL1
15 protein O-linked glycosylation GO:0006493 9.81 POGLUT1 POFUT1 EOGT
16 positive regulation of BMP signaling pathway GO:0030513 9.81 RBPJ NOTCH2 NOTCH1
17 negative regulation of cell differentiation GO:0045596 9.81 RBPJ NOTCH1 JAG1 DLL1
18 inflammatory response to antigenic stimulus GO:0002437 9.76 RBPJ NOTCH2 NOTCH1
19 cell fate determination GO:0001709 9.75 NOTCH2 JAG1 DLL1
20 negative regulation of neurogenesis GO:0050768 9.73 NOTCH1 DLL3
21 negative regulation of myoblast differentiation GO:0045662 9.73 NOTCH1 DLL1
22 pulmonary valve morphogenesis GO:0003184 9.73 NOTCH2 NOTCH1 JAG1
23 neuronal stem cell population maintenance GO:0097150 9.73 SRRT NOTCH1 JAG1 DLL1
24 regulation of Notch signaling pathway GO:0008593 9.73 RFNG POGLUT1 POFUT1 NOTCH1 MFNG LFNG
25 negative regulation of ossification GO:0030279 9.72 RBPJ NOTCH1
26 myeloid dendritic cell differentiation GO:0043011 9.72 RBPJ NOTCH2
27 positive regulation of transcription of Notch receptor target GO:0007221 9.72 RBPJ NOTCH1
28 post-anal tail morphogenesis GO:0036342 9.72 RIPPLY2 HES7
29 negative regulation of stem cell differentiation GO:2000737 9.72 NOTCH1 JAG1
30 cardiac septum morphogenesis GO:0060411 9.71 NOTCH1 JAG1
31 ventricular trabecula myocardium morphogenesis GO:0003222 9.71 RBPJ NOTCH1
32 nephron development GO:0072006 9.71 JAG1 DLL1
33 response to muramyl dipeptide GO:0032495 9.71 NOTCH1 JAG1
34 epithelial to mesenchymal transition involved in endocardial cushion formation GO:0003198 9.71 RBPJ NOTCH1
35 Notch signaling involved in heart development GO:0061314 9.71 RBPJ NOTCH2 NOTCH1 JAG1
36 cardiac left ventricle morphogenesis GO:0003214 9.7 RBPJ NOTCH1
37 morphogenesis of an epithelial sheet GO:0002011 9.7 NOTCH2 JAG1
38 left/right axis specification GO:0070986 9.7 NOTCH2 NOTCH1 DLL1
39 positive regulation of Notch signaling pathway GO:0045747 9.7 RFNG RBPJ POGLUT1 NOTCH1 MFNG JAG1
40 glomerular visceral epithelial cell development GO:0072015 9.69 NOTCH2 JAG1
41 paraxial mesoderm development GO:0048339 9.69 POGLUT1 DLL3
42 positive regulation of transcription from RNA polymerase II promoter in response to hypoxia GO:0061419 9.68 RBPJ NOTCH1
43 proximal tubule development GO:0072014 9.67 NOTCH2 DLL1
44 somite rostral/caudal axis specification GO:0032525 9.67 TBX6 RIPPLY2 MESP2
45 marginal zone B cell differentiation GO:0002315 9.67 NOTCH2 MFNG LFNG DLL1
46 ciliary body morphogenesis GO:0061073 9.66 NOTCH2 JAG1
47 regulation of developmental process GO:0050793 9.66 NOTCH2 NOTCH1
48 negative regulation of inner ear auditory receptor cell differentiation GO:0045608 9.65 NOTCH1 DLL1
49 endocardium development GO:0003157 9.65 RBPJ NOTCH1
50 regulation of somitogenesis GO:0014807 9.65 NOTCH1 LFNG DLL1

Molecular functions related to Spondylocostal Dysostosis 3, Autosomal Recessive according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 calcium ion binding GO:0005509 9.72 NOTCH2 NOTCH1 JAG1 DLL3 DLL1
2 transferase activity, transferring glycosyl groups GO:0016757 9.63 RFNG POGLUT1 POFUT1 MFNG LFNG EOGT
3 acetylglucosaminyltransferase activity GO:0008375 9.43 RFNG MFNG LFNG
4 Notch binding GO:0005112 9.26 NOTCH1 JAG1 DLL3 DLL1
5 O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity GO:0033829 8.8 RFNG MFNG LFNG
Sources

Sources for Spondylocostal Dysostosis 3, Autosomal Recessive

About this section
3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
17 EFO
18 ExPASy
19 FMA
20 GARD
28 GO
29 GTR
30 HMDB
31 HPO
32 ICD10
33 ICD10 via Orphanet
34 ICD9CM
35 IUPHAR
36 KEGG
37 LifeMap
39 LOVD
41 MedGen
44 MeSH
45 MESH via Orphanet
46 MGI
49 NCI
50 NCIt
51 NDF-RT
53 NINDS
54 Novoseek
56 OMIM via Orphanet
57 OMIM® (Updated 20-May-2021)
61 PubMed
63 QIAGEN
68 SNOMED-CT via HPO
69 Tocris
70 UMLS
71 UMLS via Orphanet
The MalaCards human disease database index: 1-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
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