PNPOD
MCID: PYR021
MIFTS: 30

Pyridoxamine 5-Prime-Phosphate Oxidase Deficiency (PNPOD)

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

Aliases & Classifications for Pyridoxamine 5-Prime-Phosphate Oxidase Deficiency

MalaCards integrated aliases for Pyridoxamine 5-Prime-Phosphate Oxidase Deficiency:

Name: Pyridoxamine 5-Prime-Phosphate Oxidase Deficiency 57 73
Pyridoxamine 5'-Phosphate Oxidase Deficiency 57 59 13
Pnpo Deficiency 57 59 75
Pnpo-Related Neonatal Epileptic Encephalopathy 59 75
Seizures, Pyridoxine-Resistant, Plp-Sensitive 57 75
Pnpod 57 75
Epileptic Encephalopathy, Neonatal, Pnpo-Related 57
Pyridoxamine-5'-Phosphate Oxidase Deficiency 37
Deficiency, Pyridoxamine 5'-Phosphate Oxidase 40
Pyridoxine-5'-Phosphate Oxidase Deficiency 75
Pyridoxal Phosphate-Responsive Seizures 59
Pyridoxal Phosphate-Dependent Seizures 59
Pyridoxamine 5'-Oxidase Deficiency 59
Pyridoxamine 5'-Phosphate Oxidase 13

Characteristics:

Orphanet epidemiological data:

59
pyridoxal phosphate-responsive seizures
Inheritance: Autosomal recessive; Prevalence: 1-9/1000000 (Europe); Age of onset: Infancy,Neonatal;

OMIM:

57
Inheritance:
autosomal recessive

Miscellaneous:
onset 0-12 hours after birth
variable features and severity


HPO:

32
pyridoxamine 5-prime-phosphate oxidase deficiency:
Inheritance autosomal recessive inheritance


Classifications:



Summaries for Pyridoxamine 5-Prime-Phosphate Oxidase Deficiency

OMIM : 57 PNPOD is an autosomal recessive inborn error of metabolism resulting in vitamin B6 deficiency that manifests as neonatal-onset severe seizures and subsequent encephalopathy. Patients with PNPO mutations tend to respond better to treatment with pyridoxal 5-prime phosphate (PLP) than with pyridoxine (summary by Plecko et al., 2014). (610090)

MalaCards based summary : Pyridoxamine 5-Prime-Phosphate Oxidase Deficiency, also known as pyridoxamine 5'-phosphate oxidase deficiency, is related to pyridoxal 5'-phosphate-dependent epilepsy and cerebral folate deficiency, and has symptoms including seizures and myoclonus. An important gene associated with Pyridoxamine 5-Prime-Phosphate Oxidase Deficiency is PNPO (Pyridoxamine 5'-Phosphate Oxidase), and among its related pathways/superpathways is Vitamin B6 metabolism. Affiliated tissues include eye and brain, and related phenotypes are abnormality of eye movement and seizures

UniProtKB/Swiss-Prot : 75 Pyridoxine-5'-phosphate oxidase deficiency: The main feature of neonatal epileptic encephalopathy is the onset within hours of birth of a severe seizure disorder that does not respond to anticonvulsant drugs and can be fatal. Seizures can cease with the administration of PLP, being resistant to treatment with pyridoxine,.

Related Diseases for Pyridoxamine 5-Prime-Phosphate Oxidase Deficiency

Diseases related to Pyridoxamine 5-Prime-Phosphate Oxidase Deficiency via text searches within MalaCards or GeneCards Suite gene sharing:

# Related Disease Score Top Affiliating Genes
1 pyridoxal 5'-phosphate-dependent epilepsy 11.9
2 cerebral folate deficiency 10.2
3 deafness with labyrinthine aplasia microtia and microdontia 10.2
4 microtia 10.2

Symptoms & Phenotypes for Pyridoxamine 5-Prime-Phosphate Oxidase Deficiency

Symptoms via clinical synopsis from OMIM:

57
Neurologic Central Nervous System:
seizures
hypertonia
myoclonus
unsteady gait
hypotonia, truncal
more
Laboratory Abnormalities:
hypoglycemia
decreased csf homovanillic acid (hva)
increased blood lactate
normal to increased plasma glycine
normal to increased plasma threonine
more
Metabolic Features:
metabolic acidosis

Prenatal Manifestations Delivery:
preterm delivery
low apgar scores

Head And Neck Eyes:
eye movement abnormalities

Growth Other:
failure to thrive

Hematology:
anemia

Abdomen Gastrointestinal:
feeding problems

Head And Neck Head:
microcephaly, progressive


Clinical features from OMIM:

610090

Human phenotypes related to Pyridoxamine 5-Prime-Phosphate Oxidase Deficiency:

59 32 (show all 33)
# Description HPO Frequency Orphanet Frequency HPO Source Accession
1 abnormality of eye movement 59 32 frequent (33%) Frequent (79-30%) HP:0000496
2 seizures 59 32 Frequent (79-30%) HP:0001250
3 failure to thrive 59 32 frequent (33%) Frequent (79-30%) HP:0001508
4 global developmental delay 59 32 frequent (33%) Frequent (79-30%) HP:0001263
5 microcephaly 59 32 occasional (7.5%) Occasional (29-5%) HP:0000252
6 hypertonia 59 32 frequent (33%) Frequent (79-30%) HP:0001276
7 hypoglycemia 59 32 frequent (33%) Frequent (79-30%) HP:0001943
8 feeding difficulties 59 32 frequent (33%) Frequent (79-30%) HP:0011968
9 myoclonus 59 32 frequent (33%) Frequent (79-30%) HP:0001336
10 increased serum lactate 59 32 frequent (33%) Frequent (79-30%) HP:0002151
11 status epilepticus 59 32 hallmark (90%) Very frequent (99-80%) HP:0002133
12 metabolic acidosis 59 32 frequent (33%) Frequent (79-30%) HP:0001942
13 premature birth 59 32 frequent (33%) Frequent (79-30%) HP:0001622
14 hypoargininemia 59 32 frequent (33%) Frequent (79-30%) HP:0005961
15 abnormality of tyrosine metabolism 59 32 occasional (7.5%) Occasional (29-5%) HP:0010917
16 pyridoxine-responsive sideroblastic anemia 59 32 occasional (7.5%) Occasional (29-5%) HP:0005522
17 unsteady gait 59 32 frequent (33%) Frequent (79-30%) HP:0002317
18 epileptic encephalopathy 59 32 hallmark (90%) Very frequent (99-80%) HP:0200134
19 muscular hypotonia of the trunk 59 32 frequent (33%) Frequent (79-30%) HP:0008936
20 global brain atrophy 59 32 frequent (33%) Frequent (79-30%) HP:0002283
21 abnormality of histidine metabolism 59 32 occasional (7.5%) Occasional (29-5%) HP:0010904
22 eeg with burst suppression 59 32 frequent (33%) Frequent (79-30%) HP:0010851
23 abnormality of the amniotic fluid 59 32 frequent (33%) Frequent (79-30%) HP:0001560
24 decreased csf homovanillic acid 59 32 frequent (33%) Frequent (79-30%) HP:0003785
25 high-pitched cry 59 32 frequent (33%) Frequent (79-30%) HP:0025430
26 low apgar score 59 32 frequent (33%) Frequent (79-30%) HP:0030917
27 abnormality of glycine metabolism 59 32 occasional (7.5%) Occasional (29-5%) HP:0010895
28 abnormality of threonine metabolism 59 32 occasional (7.5%) Occasional (29-5%) HP:0010900
29 feeding difficulties in infancy 32 HP:0008872
30 anemia 32 HP:0001903
31 encephalopathy 32 HP:0001298
32 progressive microcephaly 32 HP:0000253
33 abnormality of arginine metabolism 59 Occasional (29-5%)

UMLS symptoms related to Pyridoxamine 5-Prime-Phosphate Oxidase Deficiency:


seizures, myoclonus

Drugs & Therapeutics for Pyridoxamine 5-Prime-Phosphate Oxidase Deficiency

Search Clinical Trials , NIH Clinical Center for Pyridoxamine 5-Prime-Phosphate Oxidase Deficiency

Genetic Tests for Pyridoxamine 5-Prime-Phosphate Oxidase Deficiency

Anatomical Context for Pyridoxamine 5-Prime-Phosphate Oxidase Deficiency

MalaCards organs/tissues related to Pyridoxamine 5-Prime-Phosphate Oxidase Deficiency:

41
Eye, Brain

Publications for Pyridoxamine 5-Prime-Phosphate Oxidase Deficiency

Articles related to Pyridoxamine 5-Prime-Phosphate Oxidase Deficiency:

# Title Authors Year
1
Pyridoxine-5'-phosphate oxidase (Pnpo) deficiency: Clinical and biochemical alterations associated with the C.347g>A (P.A^Arg116gln) mutation. ( 28818555 )
2017
2
A new fatal case of pyridox(am)ine 5'-phosphate oxidase (PNPO) deficiency. ( 18024216 )
2008
3
Pyridoxal 5'-phosphate values in cerebrospinal fluid: reference values and diagnosis of PNPO deficiency in paediatric patients. ( 18294893 )
2008
4
PNPO deficiency: an under diagnosed inborn error of pyridoxine metabolism. ( 18485777 )
2008

Variations for Pyridoxamine 5-Prime-Phosphate Oxidase Deficiency

UniProtKB/Swiss-Prot genetic disease variations for Pyridoxamine 5-Prime-Phosphate Oxidase Deficiency:

75
# Symbol AA change Variation ID SNP ID
1 PNPO p.Arg229Trp VAR_029360 rs104894629
2 PNPO p.Arg225His VAR_078229 rs550423482
3 PNPO p.Arg229Gln VAR_078643 rs773450573

ClinVar genetic disease variations for Pyridoxamine 5-Prime-Phosphate Oxidase Deficiency:

6 (show top 50) (show all 136)
# Gene Variation Type Significance SNP ID Assembly Location
1 PNPO NM_018129.3(PNPO): c.685C> T (p.Arg229Trp) single nucleotide variant Pathogenic rs104894629 GRCh37 Chromosome 17, 46024047: 46024047
2 PNPO NM_018129.3(PNPO): c.685C> T (p.Arg229Trp) single nucleotide variant Pathogenic rs104894629 GRCh38 Chromosome 17, 47946681: 47946681
3 PNPO NM_018129.3(PNPO): c.364_417del54 single nucleotide variant Pathogenic rs774710082 GRCh37 Chromosome 17, 46022924: 46022924
4 PNPO NM_018129.3(PNPO): c.364_417del54 single nucleotide variant Pathogenic rs774710082 GRCh38 Chromosome 17, 47945558: 47945558
5 PNPO NM_018129.3(PNPO): c.784T> C (p.Ter262Gln) single nucleotide variant Pathogenic rs104894631 GRCh37 Chromosome 17, 46024146: 46024146
6 PNPO NM_018129.3(PNPO): c.784T> C (p.Ter262Gln) single nucleotide variant Pathogenic rs104894631 GRCh38 Chromosome 17, 47946780: 47946780
7 PNPO NM_018129.3(PNPO): c.520C> T (p.Gln174Ter) single nucleotide variant Pathogenic rs267606958 GRCh37 Chromosome 17, 46023329: 46023329
8 PNPO NM_018129.3(PNPO): c.520C> T (p.Gln174Ter) single nucleotide variant Pathogenic rs267606958 GRCh38 Chromosome 17, 47945963: 47945963
9 PNPO NM_018129.3(PNPO): c.165C> T (p.Ser55=) single nucleotide variant Benign rs11079804 GRCh37 Chromosome 17, 46020698: 46020698
10 PNPO NM_018129.3(PNPO): c.165C> T (p.Ser55=) single nucleotide variant Benign rs11079804 GRCh38 Chromosome 17, 47943332: 47943332
11 PNPO NM_018129.3(PNPO): c.347G> A (p.Arg116Gln) single nucleotide variant Benign/Likely benign rs17679445 GRCh37 Chromosome 17, 46022065: 46022065
12 PNPO NM_018129.3(PNPO): c.347G> A (p.Arg116Gln) single nucleotide variant Benign/Likely benign rs17679445 GRCh38 Chromosome 17, 47944699: 47944699
13 PNPO NM_018129.3(PNPO): c.486C> G (p.Pro162=) single nucleotide variant Benign/Likely benign rs35974730 GRCh37 Chromosome 17, 46023295: 46023295
14 PNPO NM_018129.3(PNPO): c.486C> G (p.Pro162=) single nucleotide variant Benign/Likely benign rs35974730 GRCh38 Chromosome 17, 47945929: 47945929
15 PNPO NM_018129.3(PNPO): c.552G> A (p.Leu184=) single nucleotide variant Benign/Likely benign rs4378657 GRCh37 Chromosome 17, 46023694: 46023694
16 PNPO NM_018129.3(PNPO): c.552G> A (p.Leu184=) single nucleotide variant Benign/Likely benign rs4378657 GRCh38 Chromosome 17, 47946328: 47946328
17 PNPO NM_018129.3(PNPO): c.500T> C (p.Ile167Thr) single nucleotide variant Conflicting interpretations of pathogenicity rs546737191 GRCh37 Chromosome 17, 46023309: 46023309
18 PNPO NM_018129.3(PNPO): c.500T> C (p.Ile167Thr) single nucleotide variant Conflicting interpretations of pathogenicity rs546737191 GRCh38 Chromosome 17, 47945943: 47945943
19 PNPO NM_018129.3(PNPO): c.546+15G> A single nucleotide variant Benign/Likely benign rs71377328 GRCh37 Chromosome 17, 46023370: 46023370
20 PNPO NM_018129.3(PNPO): c.546+15G> A single nucleotide variant Benign/Likely benign rs71377328 GRCh38 Chromosome 17, 47946004: 47946004
21 PNPO NM_018129.3(PNPO): c.723C> G (p.Ser241=) single nucleotide variant Conflicting interpretations of pathogenicity rs144362146 GRCh37 Chromosome 17, 46024085: 46024085
22 PNPO NM_018129.3(PNPO): c.723C> G (p.Ser241=) single nucleotide variant Conflicting interpretations of pathogenicity rs144362146 GRCh38 Chromosome 17, 47946719: 47946719
23 PNPO NM_018129.3(PNPO): c.98A> T (p.Asp33Val) single nucleotide variant Pathogenic rs370243877 GRCh37 Chromosome 17, 46019139: 46019139
24 PNPO NM_018129.3(PNPO): c.98A> T (p.Asp33Val) single nucleotide variant Pathogenic rs370243877 GRCh38 Chromosome 17, 47941773: 47941773
25 PNPO NM_018129.3(PNPO): c.167T> G (p.Leu56Arg) single nucleotide variant Uncertain significance rs145461623 GRCh37 Chromosome 17, 46020700: 46020700
26 PNPO NM_018129.3(PNPO): c.167T> G (p.Leu56Arg) single nucleotide variant Uncertain significance rs145461623 GRCh38 Chromosome 17, 47943334: 47943334
27 PNPO NM_018129.3(PNPO): c.306C> T (p.Phe102=) single nucleotide variant Benign/Likely benign rs796052866 GRCh37 Chromosome 17, 46022024: 46022024
28 PNPO NM_018129.3(PNPO): c.306C> T (p.Phe102=) single nucleotide variant Benign/Likely benign rs796052866 GRCh38 Chromosome 17, 47944658: 47944658
29 PNPO NM_018129.3(PNPO): c.448_451delCCTG (p.Pro150Argfs) deletion Pathogenic/Likely pathogenic rs796052872 GRCh37 Chromosome 17, 46023257: 46023260
30 PNPO NM_018129.3(PNPO): c.448_451delCCTG (p.Pro150Argfs) deletion Pathogenic/Likely pathogenic rs796052872 GRCh38 Chromosome 17, 47945891: 47945894
31 PNPO NM_018129.3(PNPO): c.542G> A (p.Arg181Gln) single nucleotide variant Uncertain significance rs377328326 GRCh37 Chromosome 17, 46023351: 46023351
32 PNPO NM_018129.3(PNPO): c.542G> A (p.Arg181Gln) single nucleotide variant Uncertain significance rs377328326 GRCh38 Chromosome 17, 47945985: 47945985
33 PNPO NM_018129.3(PNPO): c.544G> A (p.Glu182Lys) single nucleotide variant Uncertain significance rs138727329 GRCh37 Chromosome 17, 46023353: 46023353
34 PNPO NM_018129.3(PNPO): c.544G> A (p.Glu182Lys) single nucleotide variant Uncertain significance rs138727329 GRCh38 Chromosome 17, 47945987: 47945987
35 PNPO NM_018129.3(PNPO): c.686G> A (p.Arg229Gln) single nucleotide variant Conflicting interpretations of pathogenicity rs773450573 GRCh37 Chromosome 17, 46024048: 46024048
36 PNPO NM_018129.3(PNPO): c.686G> A (p.Arg229Gln) single nucleotide variant Conflicting interpretations of pathogenicity rs773450573 GRCh38 Chromosome 17, 47946682: 47946682
37 PNPO NM_018129.3(PNPO): c.698G> A (p.Arg233Gln) single nucleotide variant Uncertain significance rs144390543 GRCh37 Chromosome 17, 46024060: 46024060
38 PNPO NM_018129.3(PNPO): c.698G> A (p.Arg233Gln) single nucleotide variant Uncertain significance rs144390543 GRCh38 Chromosome 17, 47946694: 47946694
39 PNPO NM_018129.3(PNPO): c.782C> T (p.Pro261Leu) single nucleotide variant Uncertain significance rs769125577 GRCh37 Chromosome 17, 46024144: 46024144
40 PNPO NM_018129.3(PNPO): c.782C> T (p.Pro261Leu) single nucleotide variant Uncertain significance rs769125577 GRCh38 Chromosome 17, 47946778: 47946778
41 PNPO NM_018129.3(PNPO): c.674G> A (p.Arg225His) single nucleotide variant Pathogenic rs550423482 GRCh38 Chromosome 17, 47946670: 47946670
42 PNPO NM_018129.3(PNPO): c.674G> A (p.Arg225His) single nucleotide variant Pathogenic rs550423482 GRCh37 Chromosome 17, 46024036: 46024036
43 PNPO NM_018129.3(PNPO): c.*945C> T single nucleotide variant Uncertain significance rs886053107 GRCh38 Chromosome 17, 47947727: 47947727
44 PNPO NM_018129.3(PNPO): c.*945C> T single nucleotide variant Uncertain significance rs886053107 GRCh37 Chromosome 17, 46025093: 46025093
45 PNPO NM_018129.3(PNPO): c.*1151C> T single nucleotide variant Uncertain significance rs145323612 GRCh38 Chromosome 17, 47947933: 47947933
46 PNPO NM_018129.3(PNPO): c.*1151C> T single nucleotide variant Uncertain significance rs145323612 GRCh37 Chromosome 17, 46025299: 46025299
47 PNPO NM_018129.3(PNPO): c.*1580G> A single nucleotide variant Uncertain significance rs143175555 GRCh38 Chromosome 17, 47948362: 47948362
48 PNPO NM_018129.3(PNPO): c.*1580G> A single nucleotide variant Uncertain significance rs143175555 GRCh37 Chromosome 17, 46025728: 46025728
49 PNPO NM_018129.3(PNPO): c.*1668G> A single nucleotide variant Likely benign rs7208554 GRCh38 Chromosome 17, 47948450: 47948450
50 PNPO NM_018129.3(PNPO): c.*1668G> A single nucleotide variant Likely benign rs7208554 GRCh37 Chromosome 17, 46025816: 46025816

Expression for Pyridoxamine 5-Prime-Phosphate Oxidase Deficiency

Search GEO for disease gene expression data for Pyridoxamine 5-Prime-Phosphate Oxidase Deficiency.

Pathways for Pyridoxamine 5-Prime-Phosphate Oxidase Deficiency

Pathways related to Pyridoxamine 5-Prime-Phosphate Oxidase Deficiency according to KEGG:

37
# Name Kegg Source Accession
1 Vitamin B6 metabolism hsa00750

GO Terms for Pyridoxamine 5-Prime-Phosphate Oxidase Deficiency

Sources for Pyridoxamine 5-Prime-Phosphate Oxidase Deficiency

3 CDC
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9 Cosmic
10 dbSNP
11 DGIdb
17 ExPASy
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69 SNOMED-CT via HPO
70 SNOMED-CT via Orphanet
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74 UMLS via Orphanet
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