SMDCRD
MCID: SPN151
MIFTS: 29

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 58 54 76 38 30 6 74
Smd-Crd 54 60
Smdcrd 58 76
Spondylometaphyseal Dysplasia-Cone-Rod Dystrophy Syndrome 60
Dysplasia, Spondylometaphyseal, with Cone-Rod Dystrophy 41

Characteristics:

Orphanet epidemiological data:

60
spondylometaphyseal dysplasia-cone-rod dystrophy syndrome
Inheritance: Autosomal recessive; Prevalence: <1/1000000 (Worldwide);

OMIM:

58
Inheritance:
autosomal recessive


HPO:

33
spondylometaphyseal dysplasia with cone-rod dystrophy:
Inheritance autosomal recessive inheritance


Classifications:



Summaries for Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy

OMIM : 58 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 : 54 The following summary is from Orphanet, a European reference portal for information on rare diseases and orphan drugs.Orpha Number: 85167Disease definitionSpondylometaphyseal 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.

UniProtKB/Swiss-Prot : 76 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

Symptoms & Phenotypes for Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy

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

60 33 (show all 45)
# Description HPO Frequency Orphanet Frequency HPO Source Accession
1 bowing of the long bones 60 33 hallmark (90%) Very frequent (99-80%) HP:0006487
2 platyspondyly 60 33 hallmark (90%) Very frequent (99-80%) HP:0000926
3 rhizomelia 60 33 hallmark (90%) Very frequent (99-80%) HP:0008905
4 severe short stature 60 33 hallmark (90%) Very frequent (99-80%) HP:0003510
5 iris hypopigmentation 60 33 hallmark (90%) Very frequent (99-80%) HP:0007730
6 spondylometaphyseal dysplasia 60 33 hallmark (90%) Very frequent (99-80%) HP:0002657
7 decreased hip abduction 60 33 hallmark (90%) Very frequent (99-80%) HP:0003184
8 cone/cone-rod dystrophy 60 33 hallmark (90%) Very frequent (99-80%) HP:0000548
9 metaphyseal cupping 60 33 hallmark (90%) Very frequent (99-80%) HP:0003021
10 nystagmus 60 33 frequent (33%) Frequent (79-30%) HP:0000639
11 scoliosis 60 33 frequent (33%) Frequent (79-30%) HP:0002650
12 hyperlordosis 60 33 frequent (33%) Frequent (79-30%) HP:0003307
13 photophobia 60 33 frequent (33%) Frequent (79-30%) HP:0000613
14 myopia 60 33 frequent (33%) Frequent (79-30%) HP:0000545
15 nyctalopia 60 33 frequent (33%) Frequent (79-30%) HP:0000662
16 visual loss 60 33 frequent (33%) Frequent (79-30%) HP:0000572
17 abnormality of the ribs 60 33 frequent (33%) Frequent (79-30%) HP:0000772
18 abnormality of color vision 60 33 frequent (33%) Frequent (79-30%) HP:0000551
19 astigmatism 60 33 frequent (33%) Frequent (79-30%) HP:0000483
20 large central visual field defect 60 33 frequent (33%) Frequent (79-30%) HP:0001129
21 peripheral visual field loss 60 33 frequent (33%) Frequent (79-30%) HP:0007994
22 high hypermetropia 33 frequent (33%) HP:0008499
23 short palm 60 33 occasional (7.5%) Occasional (29-5%) HP:0004279
24 limited elbow movement 60 33 occasional (7.5%) Occasional (29-5%) HP:0002996
25 dental malocclusion 33 HP:0000689
26 hypoplastic inferior ilia 33 HP:0008821
27 joint stiffness 33 HP:0001387
28 ovoid vertebral bodies 33 HP:0003300
29 progressive visual loss 33 HP:0000529
30 growth delay 60 Very frequent (99-80%)
31 postnatal growth retardation 33 HP:0008897
32 recurrent otitis media 33 HP:0000403
33 brachydactyly 33 HP:0001156
34 abnormality of macular pigmentation 33 HP:0008002
35 high-grade hypermetropia 60 Frequent (79-30%)
36 coxa vara 33 HP:0002812
37 short finger 33 HP:0009381
38 short metacarpal 33 HP:0010049
39 cupped ribs 33 HP:0000887
40 femoral bowing 33 HP:0002980
41 tibial bowing 33 HP:0002982
42 metaphyseal widening 33 HP:0003016
43 metaphyseal irregularity 33 HP:0003025
44 severe platyspondyly 33 HP:0004565
45 narrow greater sacrosciatic notches 33 HP:0003375

Symptoms via clinical synopsis from OMIM:

58
Head And Neck Eyes:
nystagmus
macular pigmentary changes
cone-rod dystrophy
vision impairment, progressive

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

Head And Neck Ears:
recurrent otitis media

Skeletal Limbs:
femoral bowing
tibial bowing
metaphyseal cupping
rhizomelic shortening

Head And Neck Face:
normal facies

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

Growth Other:
postnatal growth retardation

Skeletal Hands:
brachydactyly
short metacarpals
thick proximal and middle phalanges

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 30 PCYT1A

Anatomical Context for Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy

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

42
Bone, Eye

Publications for Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy

Articles related to Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy:

# Title Authors Year
1
Mutations in PCYT1A Cause Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy. ( 24387991 )
2014
2
Novel mutations in PCYT1A are responsible for spondylometaphyseal dysplasia with cone-rod dystrophy. ( 24476460 )
2014
3
Mutations in PCYT1A, Encoding a Key Regulator of Phosphatidylcholine Metabolism, Cause Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy. ( 24387990 )
2014
4
Spondylometaphyseal dysplasia with cone-rod dystrophy. ( 21412974 )
2011
5
Spondylometaphyseal dysplasia with cone-rod dystrophy. ( 20141353 )
2010
6
Further delineation of spondylometaphyseal dysplasia with cone-rod dystrophy. ( 19012331 )
2008
7
Spondylometaphyseal dysplasia with cone-rod dystrophy. ( 15326626 )
2004

Variations for Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy

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

76
# 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

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

6 (show all 18)
# Gene Variation Type Significance SNP ID Assembly Location
1 PCYT1A NM_005017.3(PCYT1A): c.296C> T (p.Ala99Val) single nucleotide variant Pathogenic rs587777189 GRCh37 Chromosome 3, 195975116: 195975116
2 PCYT1A NM_005017.3(PCYT1A): c.296C> T (p.Ala99Val) single nucleotide variant Pathogenic rs587777189 GRCh38 Chromosome 3, 196248245: 196248245
3 PCYT1A NM_005017.3(PCYT1A): c.448C> G (p.Pro150Ala) single nucleotide variant Pathogenic rs587777190 GRCh37 Chromosome 3, 195974276: 195974276
4 PCYT1A NM_005017.3(PCYT1A): c.448C> G (p.Pro150Ala) single nucleotide variant Pathogenic rs587777190 GRCh38 Chromosome 3, 196247405: 196247405
5 PCYT1A NM_005017.3(PCYT1A): c.295G> A (p.Ala99Thr) single nucleotide variant Pathogenic rs587777191 GRCh37 Chromosome 3, 195975117: 195975117
6 PCYT1A NM_005017.3(PCYT1A): c.295G> A (p.Ala99Thr) single nucleotide variant Pathogenic rs587777191 GRCh38 Chromosome 3, 196248246: 196248246
7 PCYT1A NM_005017.3(PCYT1A): c.847C> T (p.Arg283Ter) single nucleotide variant Pathogenic rs587777192 GRCh37 Chromosome 3, 195966468: 195966468
8 PCYT1A NM_005017.3(PCYT1A): c.847C> T (p.Arg283Ter) single nucleotide variant Pathogenic rs587777192 GRCh38 Chromosome 3, 196239597: 196239597
9 PCYT1A NM_005017.3(PCYT1A): c.990delC (p.Ser331Profs) deletion Pathogenic rs587777193 GRCh37 Chromosome 3, 195965673: 195965673
10 PCYT1A NM_005017.3(PCYT1A): c.990delC (p.Ser331Profs) deletion Pathogenic rs587777193 GRCh38 Chromosome 3, 196238802: 196238802
11 PCYT1A NM_005017.3(PCYT1A): c.669G> C (p.Arg223Ser) single nucleotide variant Pathogenic rs540053239 GRCh37 Chromosome 3, 195968858: 195968858
12 PCYT1A NM_005017.3(PCYT1A): c.669G> C (p.Arg223Ser) single nucleotide variant Pathogenic rs540053239 GRCh38 Chromosome 3, 196241987: 196241987
13 PCYT1A NM_005017.3(PCYT1A): c.385G> A (p.Glu129Lys) single nucleotide variant Pathogenic rs587777194 GRCh37 Chromosome 3, 195974339: 195974339
14 PCYT1A NM_005017.3(PCYT1A): c.385G> A (p.Glu129Lys) single nucleotide variant Pathogenic rs587777194 GRCh38 Chromosome 3, 196247468: 196247468
15 PCYT1A NM_005017.3(PCYT1A): c.571T> C (p.Phe191Leu) single nucleotide variant Pathogenic rs587777195 GRCh37 Chromosome 3, 195968956: 195968956
16 PCYT1A NM_005017.3(PCYT1A): c.571T> C (p.Phe191Leu) single nucleotide variant Pathogenic rs587777195 GRCh38 Chromosome 3, 196242085: 196242085
17 PCYT1A NM_005017.3(PCYT1A): c.968dupG (p.Ser323Argfs) duplication Pathogenic rs587777196 GRCh37 Chromosome 3, 195965695: 195965695
18 PCYT1A NM_005017.3(PCYT1A): c.968dupG (p.Ser323Argfs) duplication Pathogenic rs587777196 GRCh38 Chromosome 3, 196238824: 196238824

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:

38
# 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
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9 Cosmic
10 dbSNP
11 DGIdb
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70 SNOMED-CT via HPO
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75 UMLS via Orphanet
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