MCID: SPN151
MIFTS: 28

Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy

Categories: Genetic diseases, Rare diseases, Bone diseases, Fetal 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 57 53 75 37 29 6 73
Smd-Crd 53 59
Smdcrd 57 75
Spondylometaphyseal Dysplasia-Cone-Rod Dystrophy Syndrome 59
Dysplasia, Spondylometaphyseal, with Cone-Rod Dystrophy 40

Characteristics:

Orphanet epidemiological data:

59
spondylometaphyseal dysplasia-cone-rod dystrophy syndrome
Inheritance: Autosomal recessive; Prevalence: <1/1000000 (Worldwide);

OMIM:

57
Inheritance:
autosomal recessive


HPO:

32
spondylometaphyseal dysplasia with cone-rod dystrophy:
Inheritance autosomal recessive inheritance


Classifications:



Summaries for Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy

OMIM : 57 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 related phenotypes are nystagmus and scoliosis

NIH Rare Diseases : 53 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 : 75 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 10.7
2 spondyloepimetaphyseal dysplasia, strudwick type 10.7

Symptoms & Phenotypes for Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy

Symptoms via clinical synopsis from OMIM:

57
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

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

59 32 (show all 45)
# Description HPO Frequency Orphanet Frequency HPO Source Accession
1 nystagmus 59 32 frequent (33%) Frequent (79-30%) HP:0000639
2 scoliosis 59 32 frequent (33%) Frequent (79-30%) HP:0002650
3 hyperlordosis 59 32 frequent (33%) Frequent (79-30%) HP:0003307
4 bowing of the long bones 59 32 hallmark (90%) Very frequent (99-80%) HP:0006487
5 photophobia 59 32 frequent (33%) Frequent (79-30%) HP:0000613
6 platyspondyly 59 32 hallmark (90%) Very frequent (99-80%) HP:0000926
7 short palm 59 32 occasional (7.5%) Occasional (29-5%) HP:0004279
8 myopia 59 32 frequent (33%) Frequent (79-30%) HP:0000545
9 nyctalopia 59 32 frequent (33%) Frequent (79-30%) HP:0000662
10 rhizomelia 59 32 hallmark (90%) Very frequent (99-80%) HP:0008905
11 visual loss 59 32 frequent (33%) Frequent (79-30%) HP:0000572
12 limited elbow movement 59 32 occasional (7.5%) Occasional (29-5%) HP:0002996
13 abnormality of the ribs 59 32 frequent (33%) Frequent (79-30%) HP:0000772
14 severe short stature 59 32 hallmark (90%) Very frequent (99-80%) HP:0003510
15 abnormality of color vision 59 32 frequent (33%) Frequent (79-30%) HP:0000551
16 iris hypopigmentation 59 32 hallmark (90%) Very frequent (99-80%) HP:0007730
17 astigmatism 59 32 frequent (33%) Frequent (79-30%) HP:0000483
18 spondylometaphyseal dysplasia 59 32 hallmark (90%) Very frequent (99-80%) HP:0002657
19 decreased hip abduction 59 32 hallmark (90%) Very frequent (99-80%) HP:0003184
20 cone/cone-rod dystrophy 59 32 hallmark (90%) Very frequent (99-80%) HP:0000548
21 metaphyseal cupping 59 32 hallmark (90%) Very frequent (99-80%) HP:0003021
22 large central visual field defect 59 32 frequent (33%) Frequent (79-30%) HP:0001129
23 peripheral visual field loss 59 32 frequent (33%) Frequent (79-30%) HP:0007994
24 dental malocclusion 32 HP:0000689
25 hypoplastic inferior ilia 32 HP:0008821
26 joint stiffness 32 HP:0001387
27 ovoid vertebral bodies 32 HP:0003300
28 progressive visual loss 32 HP:0000529
29 growth delay 59 Very frequent (99-80%)
30 postnatal growth retardation 32 HP:0008897
31 recurrent otitis media 32 HP:0000403
32 brachydactyly 32 HP:0001156
33 abnormality of macular pigmentation 32 HP:0008002
34 high-grade hypermetropia 59 Frequent (79-30%)
35 coxa vara 32 HP:0002812
36 short finger 32 HP:0009381
37 short metacarpal 32 HP:0010049
38 cupped ribs 32 HP:0000887
39 femoral bowing 32 HP:0002980
40 tibial bowing 32 HP:0002982
41 metaphyseal widening 32 HP:0003016
42 metaphyseal irregularity 32 HP:0003025
43 severe platyspondyly 32 HP:0004565
44 high hypermetropia 32 frequent (33%) HP:0008499
45 narrow greater sacrosciatic notches 32 HP:0003375

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:

41
Bone

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:

75
# 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:

37
# 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

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7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
17 ExPASy
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69 SNOMED-CT via HPO
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74 UMLS via Orphanet
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