BCYM4
MCID: BRC120
MIFTS: 25

Brachyolmia Type 4 with Mild Epiphyseal and Metaphyseal Changes (BCYM4)

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

Aliases & Classifications for Brachyolmia Type 4 with Mild Epiphyseal and Metaphyseal Changes

MalaCards integrated aliases for Brachyolmia Type 4 with Mild Epiphyseal and Metaphyseal Changes:

Name: Brachyolmia Type 4 with Mild Epiphyseal and Metaphyseal Changes 58 76
Spondyloepimetaphyseal Dysplasia, Pakistani Type 58 12 60 30 6 15 74
Brachyolmia 4 with Mild Epiphyseal and Metaphyseal Changes 58 13
Spondylodysplasia and Premature Pubarche 58 76
Semd, Pakistani Type 58 38
Bcym4 58 76
Brachyolmia, Type 4, with Mild Epiphyseal and Metaphyseal Changes 41
Spondyloepimetaphyseal Dysplasia Pakistani Type 12
Spondylometaepiphyseal Dysplasia Pakistani Type 76
Spondyloepimetaphyseal Dysplasia, Papss2 Type 60
Semd Pakistani Type 76

Characteristics:

Orphanet epidemiological data:

60
spondyloepimetaphyseal dysplasia, papss2 type
Inheritance: Autosomal recessive; Prevalence: <1/1000000 (Worldwide);

OMIM:

58
Inheritance:
autosomal recessive

Miscellaneous:
skeletal and endocrine features have not been fully characterized in all of the patients reported


HPO:

33
brachyolmia type 4 with mild epiphyseal and metaphyseal changes:
Inheritance autosomal recessive inheritance


Classifications:



External Ids:

Disease Ontology 12 DOID:0050812
OMIM 58 612847
KEGG 38 H00761
MeSH 45 D001848
ICD10 via Orphanet 35 Q77.7
UMLS via Orphanet 75 C2748515
Orphanet 60 ORPHA93282
UMLS 74 C2748515

Summaries for Brachyolmia Type 4 with Mild Epiphyseal and Metaphyseal Changes

UniProtKB/Swiss-Prot : 76 Brachyolmia type 4 with mild epiphyseal and metaphyseal changes: A form of brachyolmia, a clinically and genetically heterogeneous skeletal dysplasia primarily affecting the spine and characterized by a short trunk, short stature, and platyspondyly. BCYM4 is an autosomal recessive form with mild epiphyseal and metaphyseal changes. Clinical features include short stature evidenced at birth, short and bowed lower limbs, mild brachydactyly, kyphoscoliosis, abnormal gait, enlarged knee joints. Some BCYM4 patients may manifest premature pubarche and hyperandrogenism associated with skeletal dysplasia and short stature.

MalaCards based summary : Brachyolmia Type 4 with Mild Epiphyseal and Metaphyseal Changes, also known as spondyloepimetaphyseal dysplasia, pakistani type, is related to spondyloepimetaphyseal dysplasia, matrilin-3 related and brachyolmia type 1, hobaek type. An important gene associated with Brachyolmia Type 4 with Mild Epiphyseal and Metaphyseal Changes is PAPSS2 (3'-Phosphoadenosine 5'-Phosphosulfate Synthase 2), and among its related pathways/superpathways are Purine metabolism and Selenocompound metabolism. Affiliated tissues include bone, and related phenotypes are short stature and platyspondyly

Disease Ontology : 12 A spondyloepimetaphyseal dysplasia that is characterized by short stature, short and bowed lower limbs, mild brachydactyly, kyphoscoliosis, abnormal gait, enlarged knee joints, precocious osteoarthropathy, and normal intelligence.

OMIM : 58 This form of brachyolmia, here designated brachyolmia type 4, is characterized by short-trunk stature with normal intelligence and facies. The radiographic features include rectangular vertebral bodies with irregular endplates and narrow intervertebral discs, precocious calcification of rib cartilages, short femoral neck, mildly shortened metacarpals, and mild epiphyseal and metaphyseal changes of the tubular bones (summary by Miyake et al., 2012). (612847)

Related Diseases for Brachyolmia Type 4 with Mild Epiphyseal and Metaphyseal Changes

Diseases related to Brachyolmia Type 4 with Mild Epiphyseal and Metaphyseal Changes via text searches within MalaCards or GeneCards Suite gene sharing:

# Related Disease Score Top Affiliating Genes
1 spondyloepimetaphyseal dysplasia, matrilin-3 related 29.5 PAPSS2 SEMA3A
2 brachyolmia type 1, hobaek type 11.1

Symptoms & Phenotypes for Brachyolmia Type 4 with Mild Epiphyseal and Metaphyseal Changes

Human phenotypes related to Brachyolmia Type 4 with Mild Epiphyseal and Metaphyseal Changes:

33 (show all 13)
# Description HPO Frequency HPO Source Accession
1 short stature 33 HP:0004322
2 platyspondyly 33 HP:0000926
3 acne 33 HP:0001061
4 secondary amenorrhea 33 HP:0000869
5 kyphoscoliosis 33 HP:0002751
6 brachydactyly 33 HP:0001156
7 hirsutism 33 HP:0001007
8 irregular vertebral endplates 33 HP:0003301
9 bowing of the legs 33 HP:0002979
10 lower limb undergrowth 33 HP:0009816
11 premature pubarche 33 HP:0012411
12 spondyloepimetaphyseal dysplasia 33 HP:0002651
13 lumbar scoliosis 33 HP:0004626

Symptoms via clinical synopsis from OMIM:

58
Growth Height:
short stature

Skin Nails Hair Skin:
acne

Skin Nails Hair Hair:
hirsutism

Skeletal Limbs:
short and bowed lower limbs
enlarged knee joints
metaphyseal changes, mild, of knees and hips
osteoarthropathy, precocious

Skeletal Spine:
platyspondyly
kyphoscoliosis
lumbar scoliosis
irregular end plates

Endocrine Features:
secondary amenorrhea
hyperandrogenism
premature pubarche (in 1 female patient)

Skeletal Hands:
brachydactyly, mild

Laboratory Abnormalities:
elevated androstenedione and testosterone
dehydroepiandrosterone (dhea) at upper level of normal range
dhea sulfotransferase below limit of detection

Clinical features from OMIM:

612847

Drugs & Therapeutics for Brachyolmia Type 4 with Mild Epiphyseal and Metaphyseal Changes

Search Clinical Trials , NIH Clinical Center for Brachyolmia Type 4 with Mild Epiphyseal and Metaphyseal Changes

Genetic Tests for Brachyolmia Type 4 with Mild Epiphyseal and Metaphyseal Changes

Genetic tests related to Brachyolmia Type 4 with Mild Epiphyseal and Metaphyseal Changes:

# Genetic test Affiliating Genes
1 Spondyloepimetaphyseal Dysplasia, Pakistani Type 30 PAPSS2

Anatomical Context for Brachyolmia Type 4 with Mild Epiphyseal and Metaphyseal Changes

MalaCards organs/tissues related to Brachyolmia Type 4 with Mild Epiphyseal and Metaphyseal Changes:

42
Bone

Publications for Brachyolmia Type 4 with Mild Epiphyseal and Metaphyseal Changes

Articles related to Brachyolmia Type 4 with Mild Epiphyseal and Metaphyseal Changes:

# Title Authors Year
1
Spondyloepimetaphyseal dysplasia Pakistani type: expansion of the phenotype. ( 23633440 )
2013

Variations for Brachyolmia Type 4 with Mild Epiphyseal and Metaphyseal Changes

UniProtKB/Swiss-Prot genetic disease variations for Brachyolmia Type 4 with Mild Epiphyseal and Metaphyseal Changes:

76
# Symbol AA change Variation ID SNP ID
1 PAPSS2 p.Thr48Arg VAR_063049 rs121908951
2 PAPSS2 p.Cys43Tyr VAR_073026
3 PAPSS2 p.Leu76Gln VAR_073027
4 PAPSS2 p.Gly270Asp VAR_073029 rs138943074

ClinVar genetic disease variations for Brachyolmia Type 4 with Mild Epiphyseal and Metaphyseal Changes:

6 (show all 30)
# Gene Variation Type Significance SNP ID Assembly Location
1 PAPSS2 NM_001015880.1(PAPSS2): c.1662_1666delATTCC (p.Phe555Serfs) deletion Likely pathogenic rs797045099 GRCh37 Chromosome 10, 89504929: 89504933
2 PAPSS2 NM_001015880.1(PAPSS2): c.1662_1666delATTCC (p.Phe555Serfs) deletion Likely pathogenic rs797045099 GRCh38 Chromosome 10, 87745172: 87745176
3 PAPSS2 NM_001015880.1(PAPSS2): c.1439C> A (p.Ser480Ter) single nucleotide variant Pathogenic rs121908950 GRCh37 Chromosome 10, 89503346: 89503346
4 PAPSS2 NM_001015880.1(PAPSS2): c.1439C> A (p.Ser480Ter) single nucleotide variant Pathogenic rs121908950 GRCh38 Chromosome 10, 87743589: 87743589
5 PAPSS2 NM_001015880.1(PAPSS2): c.143C> G (p.Thr48Arg) single nucleotide variant Pathogenic rs121908951 GRCh37 Chromosome 10, 89469068: 89469068
6 PAPSS2 NM_001015880.1(PAPSS2): c.143C> G (p.Thr48Arg) single nucleotide variant Pathogenic rs121908951 GRCh38 Chromosome 10, 87709311: 87709311
7 PAPSS2 NM_004670.3(PAPSS2): c.985C> T (p.Arg329Ter) single nucleotide variant Pathogenic rs121908952 GRCh37 Chromosome 10, 89487160: 89487160
8 PAPSS2 NM_004670.3(PAPSS2): c.985C> T (p.Arg329Ter) single nucleotide variant Pathogenic rs121908952 GRCh38 Chromosome 10, 87727403: 87727403
9 PAPSS2 NM_004670.3(PAPSS2): c.337dupG (p.Ala113Glyfs) duplication Pathogenic rs606231241 GRCh38 Chromosome 10, 87713266: 87713266
10 PAPSS2 NM_004670.3(PAPSS2): c.337dupG (p.Ala113Glyfs) duplication Pathogenic rs606231241 GRCh37 Chromosome 10, 89473023: 89473023
11 PAPSS2 NM_004670.3(PAPSS2): c.616_634del19 (p.Val206Serfs) deletion Pathogenic rs606231242 GRCh38 Chromosome 10, 87714840: 87714858
12 PAPSS2 NM_004670.3(PAPSS2): c.616_634del19 (p.Val206Serfs) deletion Pathogenic rs606231242 GRCh37 Chromosome 10, 89474597: 89474615
13 PAPSS2 NM_001015880.1(PAPSS2): c.1309_1310delAG (p.Arg437Glyfs) deletion Pathogenic rs786200933 GRCh37 Chromosome 10, 89503216: 89503217
14 PAPSS2 NM_001015880.1(PAPSS2): c.1309_1310delAG (p.Arg437Glyfs) deletion Pathogenic rs786200933 GRCh38 Chromosome 10, 87743459: 87743460
15 PAPSS2 NM_004670.3(PAPSS2): c.477_480dupCGTA (p.Lys161Argfs) duplication Pathogenic rs606231243 GRCh38 Chromosome 10, 87714139: 87714142
16 PAPSS2 NM_004670.3(PAPSS2): c.477_480dupCGTA (p.Lys161Argfs) duplication Pathogenic rs606231243 GRCh37 Chromosome 10, 89473896: 89473899
17 PAPSS2 NM_001015880.1(PAPSS2): c.661delA (p.Ile221Serfs) deletion Pathogenic rs786200934 GRCh38 Chromosome 10, 87715006: 87715006
18 PAPSS2 NM_001015880.1(PAPSS2): c.661delA (p.Ile221Serfs) deletion Pathogenic rs786200934 GRCh37 Chromosome 10, 89474763: 89474763
19 PAPSS2 NM_001015880.1(PAPSS2): c.886G> A (p.Val296Met) single nucleotide variant Benign rs45467596 GRCh37 Chromosome 10, 89487046: 89487046
20 PAPSS2 NM_001015880.1(PAPSS2): c.886G> A (p.Val296Met) single nucleotide variant Benign rs45467596 GRCh38 Chromosome 10, 87727289: 87727289
21 PAPSS2 NM_001015880.1(PAPSS2): c.1403C> T (p.Ala468Val) single nucleotide variant Benign rs34097979 GRCh37 Chromosome 10, 89503310: 89503310
22 PAPSS2 NM_001015880.1(PAPSS2): c.1403C> T (p.Ala468Val) single nucleotide variant Benign rs34097979 GRCh38 Chromosome 10, 87743553: 87743553
23 PAPSS2 NM_001015880.1(PAPSS2): c.276T> C (p.Ser92=) single nucleotide variant Benign rs17124941 GRCh37 Chromosome 10, 89472962: 89472962
24 PAPSS2 NM_001015880.1(PAPSS2): c.276T> C (p.Ser92=) single nucleotide variant Benign rs17124941 GRCh38 Chromosome 10, 87713205: 87713205
25 PAPSS2 NM_001015880.1(PAPSS2): c.683_684delTT (p.Phe228Cysfs) deletion Pathogenic GRCh37 Chromosome 10, 89474785: 89474786
26 PAPSS2 NM_001015880.1(PAPSS2): c.683_684delTT (p.Phe228Cysfs) deletion Pathogenic GRCh38 Chromosome 10, 87715028: 87715029
27 PAPSS2 NM_001015880.1(PAPSS2): c.547G> A (p.Glu183Lys) single nucleotide variant Uncertain significance GRCh38 Chromosome 10, 87714771: 87714771
28 PAPSS2 NM_001015880.1(PAPSS2): c.547G> A (p.Glu183Lys) single nucleotide variant Uncertain significance GRCh37 Chromosome 10, 89474528: 89474528
29 PAPSS2 NM_001015880.1(PAPSS2): c.1849_1851delGAG (p.Glu617del) deletion Uncertain significance GRCh38 Chromosome 10, 87745959: 87745961
30 PAPSS2 NM_001015880.1(PAPSS2): c.1849_1851delGAG (p.Glu617del) deletion Uncertain significance GRCh37 Chromosome 10, 89505716: 89505718

Expression for Brachyolmia Type 4 with Mild Epiphyseal and Metaphyseal Changes

Search GEO for disease gene expression data for Brachyolmia Type 4 with Mild Epiphyseal and Metaphyseal Changes.

Pathways for Brachyolmia Type 4 with Mild Epiphyseal and Metaphyseal Changes

Pathways related to Brachyolmia Type 4 with Mild Epiphyseal and Metaphyseal Changes according to KEGG:

38
# Name Kegg Source Accession
1 Purine metabolism hsa00230
2 Selenocompound metabolism hsa00450
3 Sulfur metabolism hsa00920
4 Metabolic pathways hsa01100

GO Terms for Brachyolmia Type 4 with Mild Epiphyseal and Metaphyseal Changes

Sources for Brachyolmia Type 4 with Mild Epiphyseal and Metaphyseal Changes

3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
17 EFO
18 ExPASy
20 FMA
29 GO
30 GTR
31 HGMD
32 HMDB
33 HPO
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35 ICD10 via Orphanet
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38 KEGG
39 LifeMap
41 LOVD
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45 MeSH
46 MESH via Orphanet
47 MGI
50 NCI
51 NCIt
52 NDF-RT
55 NINDS
56 Novoseek
58 OMIM
59 OMIM via Orphanet
63 PubMed
65 QIAGEN
70 SNOMED-CT via HPO
71 SNOMED-CT via Orphanet
72 TGDB
73 Tocris
74 UMLS
75 UMLS via Orphanet
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