MCID: PYR031
MIFTS: 38

Pyruvate Dehydrogenase E3-Binding Protein Deficiency

Categories: Genetic diseases, Neuronal diseases, Metabolic diseases, Fetal diseases, Rare diseases

Aliases & Classifications for Pyruvate Dehydrogenase E3-Binding Protein Deficiency

MalaCards integrated aliases for Pyruvate Dehydrogenase E3-Binding Protein Deficiency:

Name: Pyruvate Dehydrogenase E3-Binding Protein Deficiency 57 59 75 37 29 6 40 73
Lacticacidemia Due to Pdx1 Deficiency 57 75 13
Lactic Acidemia Due to Defect in Lipoyl-Containing Component X of the Pyruvate Dehydrogenase Complex 57 75
Pdhxd 57 75
Branched Chain Alpha-Ketoacid Dehydrogenase Complex Deficiency 59
Pyruvate Dehydrogenase Complex Component E3 Deficiency 59
Pyruvate Dehydrogenase Protein X Component Deficiency 59
Glycine Cleavage System L Protein Deficiency 59
Nadh Cytochrome B5 Reductase Deficiency 73
Dihydrolipoyl Dehydrogenase Deficiency 59
Lipoamide Dehydrogenase Deficiency 59
2-Oxoglutarate Complex Deficiency 59
Diaphorase Deficiency 59

Characteristics:

Orphanet epidemiological data:

59
pyruvate dehydrogenase e3-binding protein deficiency
Inheritance: Autosomal recessive; Age of onset: Infancy,Neonatal; Age of death: adolescent,late childhood;

OMIM:

57
Inheritance:
autosomal recessive

Miscellaneous:
variable severity
onset at birth or in early childhood
phenotypic similarities to leigh syndrome
patients may or may not have dysmorphic features


HPO:

32
pyruvate dehydrogenase e3-binding protein deficiency:
Onset and clinical course variable expressivity congenital onset
Inheritance autosomal recessive inheritance


Classifications:



Summaries for Pyruvate Dehydrogenase E3-Binding Protein Deficiency

UniProtKB/Swiss-Prot : 75 Pyruvate dehydrogenase E3-binding protein deficiency: A metabolic disorder characterized by decreased activity of the pyruvate dehydrogenase complex without observable reduction in the activities of enzymes E1, E2, or E3. Clinical features include hypotonia and psychomotor retardation.

MalaCards based summary : Pyruvate Dehydrogenase E3-Binding Protein Deficiency, also known as lacticacidemia due to pdx1 deficiency, is related to lactic acidosis and methemoglobinemia due to deficiency of methemoglobin reductase, and has symptoms including ataxia, cyanosis and headache. An important gene associated with Pyruvate Dehydrogenase E3-Binding Protein Deficiency is PDHX (Pyruvate Dehydrogenase Complex Component X), and among its related pathways/superpathways are Metabolism and Viral mRNA Translation. Affiliated tissues include eye, and related phenotypes are hypertelorism and pectus excavatum

Description from OMIM: 245349

Related Diseases for Pyruvate Dehydrogenase E3-Binding Protein Deficiency

Diseases related to Pyruvate Dehydrogenase E3-Binding Protein Deficiency via text searches within MalaCards or GeneCards Suite gene sharing:

(show all 11)
# Related Disease Score Top Affiliating Genes
1 lactic acidosis 28.2 DLD PDHA1 PDHX
2 methemoglobinemia due to deficiency of methemoglobin reductase 11.2
3 dihydrolipoamide dehydrogenase deficiency 11.2
4 maple syrup urine disease 10.0
5 methemoglobinemia 10.0
6 hereditary methemoglobinemia 10.0
7 congenital methemoglobinemia 9.9
8 methemoglobinemia, beta-globin type 9.9
9 alpha-ketoglutarate dehydrogenase deficiency 9.3 DLD PDHA1
10 pyruvate dehydrogenase e1-alpha deficiency 9.2 PDHA1 PDHX
11 leigh syndrome 8.4 DLD PDHA1 PDHX

Graphical network of the top 20 diseases related to Pyruvate Dehydrogenase E3-Binding Protein Deficiency:



Diseases related to Pyruvate Dehydrogenase E3-Binding Protein Deficiency

Symptoms & Phenotypes for Pyruvate Dehydrogenase E3-Binding Protein Deficiency

Symptoms via clinical synopsis from OMIM:

57
Head And Neck Eyes:
hypertelorism
optic atrophy
epicanthal folds
abnormal ocular movements

Neurologic Central Nervous System:
seizures
ataxia
dystonia
spastic paraplegia
unsteady gait
more
Metabolic Features:
lactic acidosis
metabolic acidosis

Chest Ribs Sternum Clavicles And Scapulae:
pectus excavatum (1 patient)

Head And Neck Mouth:
high palate

Head And Neck Head:
microcephaly
trigonocephaly
frontal metopic ridge

Laboratory Abnormalities:
increased serum pyruvate
lacticacidemia
increased serum alanine
decreased activity of the pyruvate dehydrogenase (pdh) complex
decreased levels of component x protein of the pdh complex


Clinical features from OMIM:

245349

Human phenotypes related to Pyruvate Dehydrogenase E3-Binding Protein Deficiency:

32 (show all 26)
# Description HPO Frequency HPO Source Accession
1 hypertelorism 32 HP:0000316
2 pectus excavatum 32 HP:0000767
3 high palate 32 HP:0000218
4 abnormality of eye movement 32 HP:0000496
5 intellectual disability 32 HP:0001249
6 seizures 32 HP:0001250
7 ataxia 32 HP:0001251
8 global developmental delay 32 HP:0001263
9 microcephaly 32 HP:0000252
10 optic atrophy 32 HP:0000648
11 neonatal hypotonia 32 HP:0001319
12 spastic tetraplegia 32 HP:0002510
13 epicanthus 32 HP:0000286
14 poor fine motor coordination 32 HP:0007010
15 dystonia 32 HP:0001332
16 lactic acidosis 32 HP:0003128
17 metabolic acidosis 32 HP:0001942
18 spastic paraplegia 32 HP:0001258
19 partial agenesis of the corpus callosum 32 HP:0001338
20 increased serum pyruvate 32 HP:0003542
21 trigonocephaly 32 HP:0000243
22 unsteady gait 32 HP:0002317
23 hyperalaninemia 32 HP:0003348
24 decreased activity of the pyruvate dehydrogenase complex 32 HP:0002928
25 poor gross motor coordination 32 HP:0007015
26 subependymal cysts 32 HP:0002416

UMLS symptoms related to Pyruvate Dehydrogenase E3-Binding Protein Deficiency:


ataxia, cyanosis, headache, lethargy, seizures, dyspnea on exertion

Drugs & Therapeutics for Pyruvate Dehydrogenase E3-Binding Protein Deficiency

Search Clinical Trials , NIH Clinical Center for Pyruvate Dehydrogenase E3-Binding Protein Deficiency

Genetic Tests for Pyruvate Dehydrogenase E3-Binding Protein Deficiency

Genetic tests related to Pyruvate Dehydrogenase E3-Binding Protein Deficiency:

# Genetic test Affiliating Genes
1 Pyruvate Dehydrogenase E3-Binding Protein Deficiency 29 PDHX

Anatomical Context for Pyruvate Dehydrogenase E3-Binding Protein Deficiency

MalaCards organs/tissues related to Pyruvate Dehydrogenase E3-Binding Protein Deficiency:

41
Eye

Publications for Pyruvate Dehydrogenase E3-Binding Protein Deficiency

Articles related to Pyruvate Dehydrogenase E3-Binding Protein Deficiency:

# Title Authors Year
1
Novel mutation (R192C) in CYB5R3 gene causing NADH-cytochrome b5 reductase deficiency in eight Indian patients associated with autosomal recessive congenital methemoglobinemia type-I. ( 29482478 )
2018
2
Recessive congenital methemoglobinemia due to NADH-cytochrome b5 reductase deficiency associated with recurrent early pregnancy loss (REPL) in an Indian family. ( 22797852 )
2012
3
[Establishment of a cellular model with human NADH-cytochrome b5 reductase deficiency via RNA interference]. ( 18683136 )
2008
4
A case of methemoglobinemia type II due to NADH-cytochrome b5 reductase deficiency: determination of the molecular basis. ( 10874300 )
2000

Variations for Pyruvate Dehydrogenase E3-Binding Protein Deficiency

ClinVar genetic disease variations for Pyruvate Dehydrogenase E3-Binding Protein Deficiency:

6
(show all 20)
# Gene Variation Type Significance SNP ID Assembly Location
1 PDHX NG_013368.1: g.5604_20276del14673 deletion Pathogenic GRCh38 Chromosome 11, 34916733: 34931405
2 PDHX NM_003477.2(PDHX): c.965_1023del59 (p.Asp322Alafs) deletion Pathogenic GRCh38 Chromosome 11, 34978124: 34978182
3 PDHX NM_003477.2(PDHX): c.965_1023del59 (p.Asp322Alafs) deletion Pathogenic GRCh37 Chromosome 11, 34999671: 34999729
4 PDHX NM_003477.2(PDHX): c.87_90delGAAG (p.Lys30Glyfs) deletion Pathogenic rs724159828 GRCh38 Chromosome 11, 34916742: 34916745
5 PDHX NM_003477.2(PDHX): c.87_90delGAAG (p.Lys30Glyfs) deletion Pathogenic rs724159828 GRCh37 Chromosome 11, 34938289: 34938292
6 PDHX NM_003477.2(PDHX): c.641+1G> A single nucleotide variant Pathogenic rs724159829 GRCh38 Chromosome 11, 34960519: 34960519
7 PDHX NM_003477.2(PDHX): c.641+1G> A single nucleotide variant Pathogenic rs724159829 GRCh37 Chromosome 11, 34982066: 34982066
8 PDHX NM_003477.2(PDHX): c.1024-1G> A single nucleotide variant Pathogenic rs724159830 GRCh38 Chromosome 11, 34984569: 34984569
9 PDHX NM_003477.2(PDHX): c.1024-1G> A single nucleotide variant Pathogenic rs724159830 GRCh37 Chromosome 11, 35006116: 35006116
10 PDHX NM_003477.2(PDHX): c.620delC (p.Pro207Leufs) deletion Pathogenic rs724159979 GRCh38 Chromosome 11, 34960497: 34960497
11 PDHX NM_003477.2(PDHX): c.620delC (p.Pro207Leufs) deletion Pathogenic rs724159979 GRCh37 Chromosome 11, 34982044: 34982044
12 PDHX AJ298105.1: g.61273_107768del46496ins6086 deletion Pathogenic
13 PDHX NM_003477.2(PDHX): c.742C> T (p.Gln248Ter) single nucleotide variant Pathogenic rs113309941 GRCh37 Chromosome 11, 34988287: 34988287
14 PDHX NM_003477.2(PDHX): c.742C> T (p.Gln248Ter) single nucleotide variant Pathogenic rs113309941 GRCh38 Chromosome 11, 34966740: 34966740
15 PDHX NM_003477.2(PDHX): c.1183-3088_1247+760del deletion Pathogenic GRCh38 Chromosome 11, 34989227: 34993139
16 PDHX NM_003477.2(PDHX): c.1183-3088_1247+760del deletion Pathogenic GRCh37 Chromosome 11, 35010774: 35014686
17 PDHX NM_003477.2(PDHX): c.1336C> T (p.Arg446Ter) single nucleotide variant Pathogenic rs1135402725 GRCh37 Chromosome 11, 35016549: 35016549
18 PDHX NM_003477.2(PDHX): c.1336C> T (p.Arg446Ter) single nucleotide variant Pathogenic rs1135402725 GRCh38 Chromosome 11, 34995002: 34995002
19 PDHX NM_003477.2(PDHX): c.479G> A (p.Arg160His) single nucleotide variant not provided rs747386411 GRCh37 Chromosome 11, 34979067: 34979067
20 PDHX NM_003477.2(PDHX): c.479G> A (p.Arg160His) single nucleotide variant not provided rs747386411 GRCh38 Chromosome 11, 34957520: 34957520

Expression for Pyruvate Dehydrogenase E3-Binding Protein Deficiency

Search GEO for disease gene expression data for Pyruvate Dehydrogenase E3-Binding Protein Deficiency.

Pathways for Pyruvate Dehydrogenase E3-Binding Protein Deficiency

Pathways related to Pyruvate Dehydrogenase E3-Binding Protein Deficiency according to GeneCards Suite gene sharing:

# Super pathways Score Top Affiliating Genes
1
Show member pathways
13.41 APIP DLD PDHA1 PDHX
2
Show member pathways
13.14 APIP DLD PDHA1 PDHX
3
Show member pathways
12.08 DLD PDHA1 PDHX
4
Show member pathways
11.78 DLD PDHA1
5
Show member pathways
11.55 DLD PDHA1 PDHX
6
Show member pathways
11.42 DLD PDHA1
7 11.29 DLD PDHA1 PDHX
8
Show member pathways
10.99 DLD PDHA1
9
Show member pathways
10.95 DLD PDHA1 PDHX
10
Show member pathways
10.41 DLD PDHA1 PDHX

GO Terms for Pyruvate Dehydrogenase E3-Binding Protein Deficiency

Cellular components related to Pyruvate Dehydrogenase E3-Binding Protein Deficiency according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 mitochondrion GO:0005739 9.43 DLD PDHA1 PDHX
2 myelin sheath GO:0043209 9.16 DLD PDHA1
3 mitochondrial matrix GO:0005759 9.13 DLD PDHA1 PDHX
4 pyruvate dehydrogenase complex GO:0045254 8.8 DLD PDHA1 PDHX

Biological processes related to Pyruvate Dehydrogenase E3-Binding Protein Deficiency according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 pyruvate metabolic process GO:0006090 9.43 DLD PDHA1 PDHX
2 tricarboxylic acid cycle GO:0006099 9.37 DLD PDHA1
3 cellular nitrogen compound metabolic process GO:0034641 9.33 DLD PDHA1 PDHX
4 acetyl-CoA biosynthetic process from pyruvate GO:0006086 9.32 DLD PDHA1
5 regulation of acetyl-CoA biosynthetic process from pyruvate GO:0010510 9.13 DLD PDHA1 PDHX
6 mitochondrial acetyl-CoA biosynthetic process from pyruvate GO:0061732 8.8 DLD PDHA1 PDHX

Molecular functions related to Pyruvate Dehydrogenase E3-Binding Protein Deficiency according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 pyruvate dehydrogenase (NAD+) activity GO:0034604 8.8 DLD PDHA1 PDHX

Sources for Pyruvate Dehydrogenase E3-Binding Protein Deficiency

3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
17 ExPASy
19 FMA
28 GO
29 GTR
30 HGMD
31 HMDB
32 HPO
33 ICD10
34 ICD10 via Orphanet
35 ICD9CM
36 IUPHAR
37 KEGG
38 LifeMap
40 LOVD
42 MedGen
44 MeSH
45 MESH via Orphanet
46 MGI
49 NCI
50 NCIt
51 NDF-RT
54 NINDS
55 Novoseek
57 OMIM
58 OMIM via Orphanet
62 PubMed
64 QIAGEN
69 SNOMED-CT via HPO
70 SNOMED-CT via Orphanet
71 TGDB
72 Tocris
73 UMLS
74 UMLS via Orphanet
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