SMDCRD
MCID: SPN151
MIFTS: 32

Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy (SMDCRD)

Categories: Bone diseases, Eye diseases, Fetal diseases, Genetic diseases, Rare diseases

Aliases & Classifications for Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy

MalaCards integrated aliases for Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy:

Name: Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy 56 52 73 36 29 6 71
Smd-Crd 52 58
Smdcrd 56 73
Spondylometaphyseal Dysplasia-Cone-Rod Dystrophy Syndrome 58
Dysplasia, Spondylometaphyseal, with Cone-Rod Dystrophy 39

Characteristics:

Orphanet epidemiological data:

58
spondylometaphyseal dysplasia-cone-rod dystrophy syndrome
Inheritance: Autosomal recessive; Prevalence: <1/1000000 (Worldwide);

OMIM:

56
Inheritance:
autosomal recessive


HPO:

31
spondylometaphyseal dysplasia with cone-rod dystrophy:
Inheritance autosomal recessive inheritance


Classifications:

Orphanet: 58  
Rare eye diseases
Rare bone diseases
Developmental anomalies during embryogenesis


Summaries for Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy

OMIM : 56 Spondylometaphyseal dysplasia with cone-rod dystrophy (SMDCRD) is characterized by postnatal growth deficiency resulting in profound short stature, rhizomelia with bowing of the lower extremities, platyspondyly with anterior vertebral protrusions, progressive metaphyseal irregularity and cupping with shortened tubular bones, and early-onset progressive visual impairment associated with a pigmentary maculopathy and electroretinographic evidence of cone-rod dysfunction (summary by Hoover-Fong et al., 2014). Yamamoto et al. (2014) reviewed 16 reported cases of SMDCRD, noting that all affected individuals presented uniform skeletal findings, with rhizomelia and bowed lower limbs observed in the first year of life, whereas retinal dystrophy had a more variable age of onset. There was severe disproportionate short stature, with a final height of less than 100 cm; scoliosis was usually mild. Visual loss was progressive, with stabilization in adolescence. (608940)

MalaCards based summary : Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy, also known as smd-crd, is related to cone-rod dystrophy 2 and spondyloepimetaphyseal dysplasia, strudwick type. An important gene associated with Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy is PCYT1A (Phosphate Cytidylyltransferase 1, Choline, Alpha), and among its related pathways/superpathways are Phosphonate and phosphinate metabolism and Glycerophospholipid metabolism. Affiliated tissues include bone and eye, and related phenotypes are bowing of the long bones and platyspondyly

NIH Rare Diseases : 52 The following summary is from Orphanet , a European reference portal for information on rare diseases and orphan drugs. Orpha Number: 85167 Definition Spondylometaphyseal dysplasia-cone-rod dystrophy syndrome is characterised by the association of spondylometaphyseal dysplasia (marked by platyspondyly, shortening of the tubular bones and progressive metaphyseal irregularity and cupping), with postnatal growth retardation and progressive visual impairment due to cone-rod dystrophy. So far, it has been described in eight individuals. Transmission appears to be autosomal recessive . Visit the Orphanet disease page for more resources.

KEGG : 36 Spondylometaphyseal dysplasia with cone-rod dystrophy (SMD-CRD) is a rare presumed autosomal-recessive disorder with postnatal growth deficiency leading to profound short stature; rhizomelia with bowing of the lower extremities; platyspondyly with anterior vertebral protrusions; progressive metaphyseal irregularity and cupping with shortened tubular bones; and early-onset, progressive visual impairment associated with a pigmentary maculopathy and electroretinographic evidence of cone-rod dysfunction. Spondylometaphyseal dysplasias (SMDs) are a heterogeneous group of disorders radiologically characterized by platyspondyly and metaphyseal dysplasia. Extra-skeletal abnormalities associated with SMDs are uncommon. In 2004, a unique form of SMD associated with cone-rod dystrophy (CRD) was described and defined as SMD-CRD. Loss-of-function mutations in PCYT1A have been reported as the cause of SMD-CRD.

UniProtKB/Swiss-Prot : 73 Spondylometaphyseal dysplasia with cone-rod dystrophy: A disorder characterized by postnatal growth deficiency resulting in profound short stature, rhizomelia with bowing of the lower extremities, platyspondyly with anterior vertebral protrusions, progressive metaphyseal irregularity and cupping with shortened tubular bones, and early-onset progressive visual impairment associated with a pigmentary maculopathy and electroretinographic evidence of cone-rod dysfunction.

Related Diseases for Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy

Diseases related to Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy via text searches within MalaCards or GeneCards Suite gene sharing:

# Related Disease Score Top Affiliating Genes
1 cone-rod dystrophy 2 10.8
2 spondyloepimetaphyseal dysplasia, strudwick type 10.8
3 autosomal recessive disease 10.4
4 cone dystrophy 10.4
5 scoliosis 10.4
6 retinal degeneration 10.4
7 fundus dystrophy 10.4
8 pathologic nystagmus 10.4
9 muscular dystrophy 10.4
10 inherited retinal disorder 10.4

Graphical network of the top 20 diseases related to Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy:



Diseases related to Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy

Symptoms & Phenotypes for Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy

Human phenotypes related to Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy:

58 31 (show all 45)
# Description HPO Frequency Orphanet Frequency HPO Source Accession
1 bowing of the long bones 58 31 hallmark (90%) Very frequent (99-80%) HP:0006487
2 platyspondyly 58 31 hallmark (90%) Very frequent (99-80%) HP:0000926
3 rhizomelia 58 31 hallmark (90%) Very frequent (99-80%) HP:0008905
4 iris hypopigmentation 58 31 hallmark (90%) Very frequent (99-80%) HP:0007730
5 spondylometaphyseal dysplasia 58 31 hallmark (90%) Very frequent (99-80%) HP:0002657
6 severe short stature 58 31 hallmark (90%) Very frequent (99-80%) HP:0003510
7 decreased hip abduction 58 31 hallmark (90%) Very frequent (99-80%) HP:0003184
8 cone/cone-rod dystrophy 58 31 hallmark (90%) Very frequent (99-80%) HP:0000548
9 metaphyseal cupping 58 31 hallmark (90%) Very frequent (99-80%) HP:0003021
10 scoliosis 58 31 frequent (33%) Frequent (79-30%) HP:0002650
11 nystagmus 58 31 frequent (33%) Frequent (79-30%) HP:0000639
12 hyperlordosis 58 31 frequent (33%) Frequent (79-30%) HP:0003307
13 nyctalopia 58 31 frequent (33%) Frequent (79-30%) HP:0000662
14 photophobia 58 31 frequent (33%) Frequent (79-30%) HP:0000613
15 myopia 58 31 frequent (33%) Frequent (79-30%) HP:0000545
16 visual loss 58 31 frequent (33%) Frequent (79-30%) HP:0000572
17 abnormality of the ribs 58 31 frequent (33%) Frequent (79-30%) HP:0000772
18 peripheral visual field loss 58 31 frequent (33%) Frequent (79-30%) HP:0007994
19 large central visual field defect 58 31 frequent (33%) Frequent (79-30%) HP:0001129
20 high hypermetropia 58 31 frequent (33%) Frequent (79-30%) HP:0008499
21 astigmatism 58 31 frequent (33%) Frequent (79-30%) HP:0000483
22 color vision defect 31 frequent (33%) HP:0000551
23 short palm 58 31 occasional (7.5%) Occasional (29-5%) HP:0004279
24 limited elbow movement 58 31 occasional (7.5%) Occasional (29-5%) HP:0002996
25 hypoplastic inferior ilia 31 HP:0008821
26 dental malocclusion 31 HP:0000689
27 joint stiffness 31 HP:0001387
28 brachydactyly 31 HP:0001156
29 short metacarpal 31 HP:0010049
30 ovoid vertebral bodies 31 HP:0003300
31 progressive visual loss 31 HP:0000529
32 growth delay 58 Very frequent (99-80%)
33 postnatal growth retardation 31 HP:0008897
34 recurrent otitis media 31 HP:0000403
35 abnormality of color vision 58 Frequent (79-30%)
36 abnormality of macular pigmentation 31 HP:0008002
37 coxa vara 31 HP:0002812
38 short finger 31 HP:0009381
39 cupped ribs 31 HP:0000887
40 femoral bowing 31 HP:0002980
41 tibial bowing 31 HP:0002982
42 metaphyseal widening 31 HP:0003016
43 metaphyseal irregularity 31 HP:0003025
44 severe platyspondyly 31 HP:0004565
45 narrow greater sacrosciatic notches 31 HP:0003375

Symptoms via clinical synopsis from OMIM:

56
Skeletal Spine:
scoliosis
mild platyspondyly (infancy)
ovoid vertebral bodies (infancy)
severe platyspondyly (childhood)

Skeletal Pelvis:
hypoplastic inferior ilia
coxa vara
flat acetabuli
narrowed sacrosciatic notch

Growth Other:
postnatal growth retardation

Skeletal Limbs:
femoral bowing
tibial bowing
metaphyseal cupping
rhizomelic shortening

Head And Neck Face:
normal facies

Head And Neck Eyes:
nystagmus
macular pigmentary changes
cone-rod dystrophy
vision impairment, progressive

Skeletal Hands:
brachydactyly
short metacarpals
thick proximal and middle phalanges

Head And Neck Ears:
recurrent otitis media

Head And Neck Teeth:
malocclusion

Chest Ribs Sternum Clavicles And Scapulae:
rib cupping

Clinical features from OMIM:

608940

Drugs & Therapeutics for Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy

Search Clinical Trials , NIH Clinical Center for Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy

Genetic Tests for Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy

Genetic tests related to Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy:

# Genetic test Affiliating Genes
1 Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy 29 PCYT1A

Anatomical Context for Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy

MalaCards organs/tissues related to Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy:

40
Bone, Eye

Publications for Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy

Articles related to Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy:

# Title Authors PMID Year
1
Mutations in PCYT1A, encoding a key regulator of phosphatidylcholine metabolism, cause spondylometaphyseal dysplasia with cone-rod dystrophy. 61 56 6
24387990 2014
2
Mutations in PCYT1A cause spondylometaphyseal dysplasia with cone-rod dystrophy. 61 56 6
24387991 2014
3
Spondylometaphyseal dysplasia with cone-rod dystrophy. 61 56 6
21412974 2011
4
Spondylometaphyseal dysplasia with cone-rod dystrophy. 61 56 6
15326626 2004
5
Further delineation of spondylometaphyseal dysplasia with cone-rod dystrophy. 61 56
19012331 2008
6
Disease-linked mutations in the phosphatidylcholine regulatory enzyme CCTα impair enzymatic activity and fold stability. 61
30559292 2019
7
Inborn errors of metabolism in the biosynthesis and remodelling of phospholipids. 61
25178427 2015
8
Novel mutations in PCYT1A are responsible for spondylometaphyseal dysplasia with cone-rod dystrophy. 61
24476460 2014
9
Spondylometaphyseal dysplasia with cone-rod dystrophy. 61
20141353 2010

Variations for Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy

ClinVar genetic disease variations for Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy:

6 ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎
# Gene Name Type Significance ClinVarId dbSNP ID GRCh37 Pos GRCh38 Pos
1 PCYT1A NM_001312673.2(PCYT1A):c.296C>T (p.Ala99Val)SNV Pathogenic 101057 rs587777189 3:195975116-195975116 3:196248245-196248245
2 PCYT1A NM_001312673.2(PCYT1A):c.448C>G (p.Pro150Ala)SNV Pathogenic 101058 rs587777190 3:195974276-195974276 3:196247405-196247405
3 PCYT1A NM_001312673.2(PCYT1A):c.295G>A (p.Ala99Thr)SNV Pathogenic 101059 rs587777191 3:195975117-195975117 3:196248246-196248246
4 PCYT1A NM_001312673.2(PCYT1A):c.847C>T (p.Arg283Ter)SNV Pathogenic 101060 rs587777192 3:195966468-195966468 3:196239597-196239597
5 PCYT1A NM_001312673.2(PCYT1A):c.990del (p.Ser331fs)deletion Pathogenic 101061 rs587777193 3:195965673-195965673 3:196238802-196238802
6 PCYT1A NM_001312673.2(PCYT1A):c.669G>C (p.Arg223Ser)SNV Pathogenic 101062 rs540053239 3:195968858-195968858 3:196241987-196241987
7 PCYT1A NM_001312673.2(PCYT1A):c.385G>A (p.Glu129Lys)SNV Pathogenic 101063 rs587777194 3:195974339-195974339 3:196247468-196247468
8 PCYT1A NM_001312673.2(PCYT1A):c.571T>C (p.Phe191Leu)SNV Pathogenic 101064 rs587777195 3:195968956-195968956 3:196242085-196242085
9 PCYT1A NM_001312673.2(PCYT1A):c.968dup (p.Ser323fs)duplication Pathogenic 101065 rs587777196 3:195965694-195965695 3:196238823-196238824

UniProtKB/Swiss-Prot genetic disease variations for Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy:

73
# Symbol AA change Variation ID SNP ID
1 PCYT1A p.Ala99Thr VAR_071083 rs587777191
2 PCYT1A p.Ala99Val VAR_071084 rs587777189
3 PCYT1A p.Glu129Lys VAR_071085 rs587777194
4 PCYT1A p.Pro150Ala VAR_071086 rs587777190
5 PCYT1A p.Phe191Leu VAR_071087 rs587777195
6 PCYT1A p.Arg223Ser VAR_071088 rs540053239

Expression for Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy

Search GEO for disease gene expression data for Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy.

Pathways for Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy

Pathways related to Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy according to KEGG:

36
# Name Kegg Source Accession
1 Phosphonate and phosphinate metabolism hsa00440
2 Glycerophospholipid metabolism hsa00564

GO Terms for Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy

Sources for Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy

3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
17 EFO
18 ExPASy
19 FMA
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
43 MeSH
44 MESH via Orphanet
45 MGI
48 NCI
49 NCIt
50 NDF-RT
53 NINDS
54 Novoseek
56 OMIM
57 OMIM via Orphanet
61 PubMed
63 QIAGEN
68 SNOMED-CT via HPO
69 TGDB
70 Tocris
71 UMLS
72 UMLS via Orphanet
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