IMD47
MCID: IMM140
MIFTS: 59

Immunodeficiency 47 (IMD47)

Categories: Cardiovascular diseases, Eye diseases, Fetal diseases, Genetic diseases, Immune diseases, Liver diseases, Metabolic diseases, Neuronal diseases, Rare diseases, Skin diseases
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Aliases & Classifications for Immunodeficiency 47

MalaCards integrated aliases for Immunodeficiency 47:

Name: Immunodeficiency 47 57 11 73 28 5 14
Congenital Disorder of Glycosylation Type Ii 11 58 73 5 43 14 16
Congenital Disorder of Glycosylation, Type Ii 57 12 5 71
Congenital Disorder of Glycosylation Type Iie 11 58 73 14
Cdg2e 57 11 58 73
Immunodeficiency and Hepatopathy with or Without Neurologic Features 57 11 73
Congenital Disorder of Glycosylation, Type Iie 57 12 5
Congenital Disorder of Glycosylation Type 2e 58 43 71
Cdg Iis 57 11 73
Cdg Iie 57 11 73
Cdgiis 57 11 73
Imd47 57 11 73
Cdg2s 57 11 73
Cdg1i 57 58 73
Carbohydrate Deficient Glycoprotein Syndrome Type Iie 11 58
Congenital Disorder of Glycosylation, Type Iis 57 73
Congenital Disorder of Glycosylation Ii 11 14
Congenital Disorder of Glycosylation 1i 11 73
Cdg Syndrome Type Iie 11 58
Cdg-Iie 58 73
Cdg Ii 57 73
Cdgiie 57 73
Cdg-Ii 58 73
Cdgii 57 73
Carbohydrate Deficient Glycoprotein Syndrome Type Ii 58
Glycosylation, Congenital Disorder of, Type Iie 38
Glycosylation, Congenital Disorder of, Type Ii 38
Congenital Disorder of Glycosylation Type Iis 11
Congenital Disorders of Glycosylation Type Ii 5
Congenital Disorder of Glycosylation Type 2a 71
Congenital Disorder of Glycosylation Type 1i 58
Congenital Disorder of Glycosylation 2e 73
Congenital Disorder of Glycosylation 2s 73
Mannosyltransferase 2 Deficiency 58
Immunodeficiency, Type 47 38
Cdg Syndrome Type Ii 58
Cog7-Cdg 58
Alg2-Cdg 58
Cdgiide 11

Characteristics:


Inheritance:

Immunodeficiency 47: X-linked recessive 57
Cog7-Cdg: Autosomal recessive 58
Alg2-Cdg: Autosomal recessive 58

Prevelance:

Cog7-Cdg: <1/1000000 (Worldwide) 58
Alg2-Cdg: <1/1000000 (Worldwide) 58

Age Of Onset:

Cog7-Cdg: Infancy,Neonatal 58
Alg2-Cdg: Infancy,Neonatal 58

OMIM®:

57 (Updated 08-Dec-2022)
Miscellaneous:
variable severity


Classifications:

Orphanet: 58  
Rare neurological diseases
Rare eye diseases
Rare cardiac malformations
Rare hepatic diseases
Rare skin diseases
Inborn errors of metabolism
Developmental anomalies during embryogenesis


External Ids:

OMIM Phenotypic Series 57 PS212065 PS212066 PS212066,PS300755
SNOMED-CT 68 717773005
ICD10 via Orphanet 32 E77.8
UMLS via Orphanet 72 C1842836 C2931010
UMLS 71 C1842836 C2931008 C2931010 more

Summaries for Immunodeficiency 47

UniProtKB/Swiss-Prot 73 Immunodeficiency 47: A complex immunodeficiency syndrome characterized by hypogammaglobulinemia, recurrent bacterial infections, defective glycosylation of serum proteins, and liver disease with neonatal jaundice and hepatosplenomegaly. Some patients may also have neurologic features, including seizures, mild intellectual disability, and behavioral abnormalities. Inheritance is X-linked recessive.

Congenital disorder of glycosylation 1i: A form of congenital disorder of glycosylation, a multisystem disorder caused by a defect in glycoprotein biosynthesis and characterized by under-glycosylated serum glycoproteins. Congenital disorders of glycosylation result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency. The broad spectrum of features reflects the critical role of N-glycoproteins during embryonic development, differentiation, and maintenance of cell functions.

Congenital disorder of glycosylation 2e: A multisystem disorder caused by a defect in glycoprotein biosynthesis and characterized by under-glycosylated serum glycoproteins. Congenital disorders of glycosylation result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency. The broad spectrum of features reflects the critical role of N-glycoproteins during embryonic development, differentiation, and maintenance of cell functions.

MalaCards based summary: Immunodeficiency 47, also known as congenital disorder of glycosylation type ii, is related to congenital disorder of glycosylation, type iil and congenital disorder of glycosylation, type iij, and has symptoms including seizures An important gene associated with Immunodeficiency 47 is ATP6AP1 (ATPase H+ Transporting Accessory Protein 1), and among its related pathways/superpathways are Metabolism of proteins and Disease. Affiliated tissues include liver, skin and eye, and related phenotypes are failure to thrive and hypotonia

OMIM® 57 Immunodeficiency 47: Immunodeficiency-47 (IMD47) is an X-linked recessive complex syndrome characterized by liver dysfunction, recurrent bacterial infections, hypogammaglobulinemia, and defective glycosylation of serum proteins. Some patients also have neurologic abnormalities (summary by Jansen et al., 2016).

Congenital disorder of glycosylation, type ii: Congenital disorder of glycosylation type Ii (CDG1I) is a rare autosomal recessive disorder characterized by neurologic involvement, including a convulsive syndrome of unknown origin, axial hypotonia, and mental and motor regression (summary by Papazoglu et al., 2021). For a general discussion of CDGs, see CDG1A (212065).

Congenital disorder of glycosylation, type iie: CDG IIe is caused by a mutation that impairs the integrity of the conserved oligomeric Golgi (COG) complex and alters Golgi trafficking, resulting in the disruption of multiple glycosylation pathways. For a general discussion of CDGs, see CDG1A (212065).

Disease Ontology 11 Immunodeficiency 47: A primary immunodeficiency disease characterized by liver dysfunction, recurrent bacterial infections, hypogammaglobulinemia, and defective glycosylation of serum proteins that has material basis in hemizygous mutation in ATP6AP1 on chromosome Xq28.

Congenital disorder of glycosylation type ii: A congenital disorder of glycosylation that involves malfunctioning trimming or processing of the protein-bound oligosaccharide chain.

Congenital disorder of glycosylation type iie: A congenital disorder of glycosylation type II that has material basis in a mutation of COG7 on chromosome 16p12.2.

Congenital disorder of glycosylation ii: A congenital disorder of glycosylation I that is characterized by iris coloboma, cataract, infantile spasms, developmental delay and abnormal coagulation factors and has material basis in compound heterozygous mutation in the ALG2 gene on chromosome 9q22.

Orphanet 58 Alg2-cdg: A form of congenital disorders of N-linked glycosylation characterized by iris coloboma, cataract, infantile spasms, developmental delay and abnormal coagulation factors. The disease is caused by loss-of-function mutations in the gene ALG2 (9q31.1). Transmission is autosomal recessive.

Cog7-cdg: COG7-CDG is a congenital disorder of glycosylation characterised by dysmorphism, skeletal dysplasia, hypotonia, hepatosplenomegaly, jaundice, cardiac insufficiency, recurrent infections and epilepsy. To date, it has been described in two infants, both of whom died within the first three months of life. The syndrome is caused by a mutation in the gene encoding COG-7 (chromosome 16), a subunit of the oligomeric Golgi complex.

Related Diseases for Immunodeficiency 47

Diseases related to Immunodeficiency 47 via text searches within MalaCards or GeneCards Suite gene sharing:

(show top 50) (show all 64)
# Related Disease Score Top Affiliating Genes
1 congenital disorder of glycosylation, type iil 32.5 COG7 COG1
2 congenital disorder of glycosylation, type iij 32.5 TMEM165 COG7 COG1 ALG2
3 congenital disorder of glycosylation, type iih 32.5 SRD5A3 COG7 COG1 ALG2
4 congenital disorder of glycosylation, type iim 32.4 SRD5A3 ALG6
5 congenital disorder of glycosylation, type iid 32.4 SLC35C1 SLC35A1 MPI COG1 B4GALT1 ALG2
6 congenital disorder of glycosylation, type iib 32.3 SLC35C1 SLC35A1 MAN1B1 B4GALT1 ALG2 ALG1
7 congenital disorder of glycosylation, type iia 32.3 SLC35C1 SLC35A1 MPI COG1 B4GALT1 ALG2
8 congenital disorder of glycosylation, type iin 32.3 TMEM165 SLC35C1 PGM1 MPI ALG8 ALG6
9 congenital disorder of glycosylation, type iik 32.2 TMEM165 SLC35C1 PGM1 COG1 ATP6V0A2 ALG8
10 congenital disorder of glycosylation, type iii 32.2 SRD5A3 COG7 COG1 B4GALT1 ALG8 ALG6
11 congenital disorder of glycosylation, type iip 32.2 TMEM199 PGM1 CCDC115 ATP6V0A2 ATP6AP1 ALG8
12 congenital disorder of glycosylation, type iio 32.1 TMEM199 SLC35C1 MPI CCDC115 ATP6V0A2 ATP6AP1
13 congenital disorder of glycosylation, type iif 32.1 SLC35C1 SLC35A1 MPI MAN1B1 COG1 B4GALT1
14 developmental and epileptic encephalopathy 36 30.5 SRD5A3 SLC35C1 SLC35A1 ALG8 ALG6 ALG1
15 saul-wilson syndrome 30.2 COG7 COG1
16 congenital disorder of glycosylation, type in 29.8 TMEM199 TMEM165 SRD5A3 SLC35C1 SLC35A1 PGM1
17 man1b1-cdg 11.5
18 congenital disorder of glycosylation, type iig 11.3
19 congenital disorder of glycosylation, type iic 11.3
20 congenital disorder of glycosylation, type iiq 11.3
21 congenital disorder of glycosylation, type ic 11.1
22 congenital disorder of glycosylation, type ih 10.4 ALG8 ALG2
23 cholesterol ester storage disease 10.4 TMEM199 CCDC115
24 developmental and epileptic encephalopathy 42 10.4 TMEM165 SLC35C1
25 geroderma osteodysplasticum 10.4 COG7 ATP6V0A2 ALG2
26 congenital disorder of glycosylation, type im 10.4 SRD5A3 ALG6
27 myasthenic syndrome, congenital, 15 10.4 ATP6AP1 ALG1
28 cutis laxa 10.3 ATP6V0A2 ATP6AP1 ALG2
29 schneckenbecken dysplasia 10.3 TMEM165 SLC35C1 SLC35A1 ALG6
30 ngly1-deficiency 10.3 SRD5A3 ALG1
31 fructose-1,6-bisphosphatase deficiency 10.3 PGM1 ALG2
32 peripheral nervous system disease 10.3
33 neuropathy 10.3
34 protein-losing enteropathy 10.3 SRD5A3 MPI ALG8 ALG6
35 congenital disorder of glycosylation, type ia 10.3 MPI ALG6
36 immunodeficiency 23 10.3 TMEM165 SLC35C1 MPI ALG6 ALG1
37 autosomal recessive cutis laxa type ii classic type 10.3 ATP6V0A2 ATP6AP1
38 myopathy, x-linked, with excessive autophagy 10.3 TMEM199 CCDC115
39 fructose intolerance, hereditary 10.2 SLC35C1 MPI MAN1B1 B4GALT1 ATP6AP1 ALG6
40 sialuria 10.2 SLC35A1 APOC3
41 walker-warburg syndrome 10.2 SRD5A3 SLC35C1 SLC35A1 MPI ATP6V0A2 ALG6
42 anemia, congenital dyserythropoietic, type ii 10.2
43 cerebellar hypoplasia 10.2
44 congenital dyserythropoietic anemia 10.2
45 hypotonia 10.1
46 congenital disorders of n-linked glycosylation and multiple pathway 10.1
47 wrinkly skin syndrome 10.1 ATP6V0A2 ALG2
48 congenital disorder of glycosylation, type ix 10.1
49 twin-reversed arterial perfusion sequence 10.1
50 hypercholesterolemia, familial, 1 10.0

Graphical network of the top 20 diseases related to Immunodeficiency 47:



Diseases related to Immunodeficiency 47

Symptoms & Phenotypes for Immunodeficiency 47

Human phenotypes related to Immunodeficiency 47:

58 30 (show top 50) (show all 139)
# Description HPO Frequency Orphanet Frequency HPO Source Accession
1 failure to thrive 58 30 Very rare (1%) Very frequent (99-80%)
HP:0001508
2 hypotonia 58 30 Very rare (1%) Very frequent (99-80%)
HP:0001252
3 postnatal growth retardation 58 30 Hallmark (90%) Very frequent (99-80%)
HP:0008897
4 elevated hepatic transaminase 58 30 Hallmark (90%) Very frequent (99-80%)
HP:0002910
5 feeding difficulties 58 30 Hallmark (90%) Very frequent (99-80%)
HP:0011968
6 recurrent infections 58 30 Hallmark (90%) Very frequent (99-80%)
HP:0002719
7 abnormal enzyme/coenzyme activity 58 30 Hallmark (90%) Very frequent (99-80%)
HP:0012379
8 recurrent fever 58 30 Hallmark (90%) Very frequent (99-80%)
HP:0001954
9 type i transferrin isoform profile 58 30 Very rare (1%) Very frequent (99-80%)
HP:0003642
10 type ii transferrin isoform profile 58 30 Very rare (1%) Very frequent (99-80%)
HP:0012301
11 intellectual disability 58 30 Frequent (33%) Frequent (79-30%)
HP:0001249
12 seizure 58 30 Very rare (1%) Frequent (79-30%)
Frequent (79-30%)
HP:0001250
13 cataract 58 30 Frequent (33%) Frequent (79-30%)
HP:0000518
14 wide nasal bridge 58 30 Very rare (1%) Frequent (79-30%)
HP:0000431
15 abnormal facial shape 58 30 Frequent (33%) Frequent (79-30%)
Frequent (79-30%)
HP:0001999
16 microcephaly 58 30 Very rare (1%) Frequent (79-30%)
HP:0000252
17 epicanthus 58 30 Very rare (1%) Frequent (79-30%)
HP:0000286
18 elevated circulating creatine kinase concentration 58 30 Frequent (33%) Frequent (79-30%)
HP:0003236
19 jaundice 58 30 Frequent (33%) Frequent (79-30%)
HP:0000952
20 downslanted palpebral fissures 58 30 Frequent (33%) Frequent (79-30%)
HP:0000494
21 iris coloboma 58 30 Very rare (1%) Frequent (79-30%)
HP:0000612
22 areflexia 58 30 Frequent (33%) Frequent (79-30%)
HP:0001284
23 abnormality of the kidney 58 30 Frequent (33%) Frequent (79-30%)
HP:0000077
24 hyporeflexia 58 30 Frequent (33%) Frequent (79-30%)
HP:0001265
25 severe global developmental delay 58 30 Very rare (1%) Frequent (79-30%)
HP:0011344
26 abnormality of coagulation 58 30 Frequent (33%) Frequent (79-30%)
HP:0001928
27 abnormal heart morphology 58 30 Frequent (33%) Frequent (79-30%)
HP:0001627
28 diarrhea 58 30 Very rare (1%) Frequent (79-30%)
HP:0002014
29 small for gestational age 58 30 Frequent (33%) Frequent (79-30%)
HP:0001518
30 excessive wrinkled skin 58 30 Frequent (33%) Frequent (79-30%)
HP:0007392
31 esotropia 58 30 Frequent (33%) Frequent (79-30%)
HP:0000565
32 hypsarrhythmia 58 30 Very rare (1%) Frequent (79-30%)
HP:0002521
33 progressive microcephaly 58 30 Frequent (33%) Frequent (79-30%)
HP:0000253
34 primary microcephaly 30 Frequent (33%) HP:0011451
35 short neck 58 30 Occasional (7.5%) Occasional (29-5%)
HP:0000470
36 hepatomegaly 58 30 Very rare (1%) Occasional (29-5%)
Frequent (79-30%)
HP:0002240
37 retrognathia 58 30 Occasional (7.5%) Occasional (29-5%)
HP:0000278
38 micrognathia 58 30 Occasional (7.5%) Occasional (29-5%)
HP:0000347
39 narrow mouth 58 30 Occasional (7.5%) Occasional (29-5%)
HP:0000160
40 adducted thumb 58 30 Occasional (7.5%) Occasional (29-5%)
HP:0001181
41 infantile spasms 58 30 Very rare (1%) Occasional (29-5%)
HP:0012469
42 cerebellar atrophy 58 30 Occasional (7.5%) Occasional (29-5%)
HP:0001272
43 hepatosplenomegaly 58 30 Occasional (7.5%) Occasional (29-5%)
HP:0001433
44 hypoplasia of the corpus callosum 58 30 Occasional (7.5%) Occasional (29-5%)
HP:0002079
45 long fingers 58 30 Occasional (7.5%) Occasional (29-5%)
HP:0100807
46 subcortical cerebral atrophy 58 30 Occasional (7.5%) Occasional (29-5%)
HP:0012157
47 cerebral hypomyelination 58 30 Occasional (7.5%) Occasional (29-5%)
HP:0006808
48 abnormal basal ganglia mri signal intensity 58 30 Occasional (7.5%) Occasional (29-5%)
HP:0012751
49 widened subarachnoid space 58 30 Occasional (7.5%) Occasional (29-5%)
HP:0012704
50 hyperintensity of cerebral white matter on mri 58 30 Occasional (7.5%) Occasional (29-5%)
HP:0030890

Symptoms via clinical synopsis from OMIM®:

57 (Updated 08-Dec-2022)
Abdomen Spleen:
splenomegaly

Skin Nails Hair Hair:
alopecia

Immunology:
leukopenia
recurrent bacterial infections
hypogammaglobulinemia
poor response to vaccination

Laboratory Abnormalities:
abnormal liver enzymes
low serum copper
low serum ceruloplasmin
defective n- and o-glycosylation of serum proteins
high alkaline phosphatase

Head And Neck Ears:
hearing loss, sensorineural (1 family)

Cardiovascular Heart:
dilated aortic sinus (in 1 patient)

Abdomen Pancreas:
exocrine pancreatic insufficiency (one patient)

Abdomen Liver:
hepatomegaly
hepatic fibrosis
cirrhosis
steatosis
abnormal mitochondria
more
Skin Nails Hair Skin:
cutis laxa
jaundice, neonatal
cutis aplasia (one patient)

Neurologic Central Nervous System:
seizures (in some patients)
intellectual disability (in some patients)

Neurologic Behavioral Psychiatric Manifestations:
behavioral abnormalities (in some patients)

Head And Neck Eyes:
hyperopia (1 family)

Chest Diaphragm:
diaphragmatic hernia (in 1 patient)

Clinical features from OMIM®:

300972 607906 608779 (Updated 08-Dec-2022)

UMLS symptoms related to Immunodeficiency 47:


seizures

GenomeRNAi Phenotypes related to Immunodeficiency 47 according to GeneCards Suite gene sharing:

25
# Description GenomeRNAi Source Accession Score Top Affiliating Genes
1 no effect GR00402-S-1 10.2 ALG1 ALG2 ALG6 ALG8 APOC3 ATP6AP1
2 no effect GR00402-S-2 10.2 ALG1 ALG2 ALG6 ALG8 APOC3 ATP6AP1

MGI Mouse Phenotypes related to Immunodeficiency 47:

45
# Description MGI Source Accession Score Top Affiliating Genes
1 mortality/aging MP:0010768 9.5 ALG1 ALG2 ALG6 ALG8 ATP6AP1 B4GALT1

Drugs & Therapeutics for Immunodeficiency 47

Search Clinical Trials, NIH Clinical Center for Immunodeficiency 47

Cochrane evidence based reviews: congenital disorder of glycosylation type ii

Genetic Tests for Immunodeficiency 47

Genetic tests related to Immunodeficiency 47:

# Genetic test Affiliating Genes
1 Immunodeficiency 47 28 ATP6AP1

Anatomical Context for Immunodeficiency 47

Organs/tissues related to Immunodeficiency 47:

MalaCards : Liver, Skin, Eye, Kidney, Heart, Brain, Skeletal Muscle
ODiseA: Blood And Bone Marrow, Brain, Kidney

Publications for Immunodeficiency 47

Articles related to Immunodeficiency 47:

(show top 50) (show all 80)
# Title Authors PMID Year
1
Severe phenotype of ATP6AP1-CDG in two siblings with a novel mutation leading to a differential tissue-specific ATP6AP1 protein pattern, cellular oxidative stress and hepatic copper accumulation. 57 5
32216104 2020
2
Prenatal and postnatal phenotype of a pathologic variant in the ATP6AP1 gene. 57 5
32058063 2020
3
Expanding the phenotype of metabolic cutis laxa with an additional disorder of N-linked protein glycosylation. 57 5
29192153 2018
4
Cutis laxa, exocrine pancreatic insufficiency and altered cellular metabolomics as additional symptoms in a new patient with ATP6AP1-CDG. 57 5
29396028 2018
5
ATP6AP1 deficiency causes an immunodeficiency with hepatopathy, cognitive impairment and abnormal protein glycosylation. 57 5
27231034 2016
6
Mass spectrometry glycophenotype characterization of ALG2-CDG in Argentinean patients with a new genetic variant in homozygosis. 62 5
33644825 2021
7
A common mutation in the COG7 gene with a consistent phenotype including microcephaly, adducted thumbs, growth retardation, VSD and episodes of hyperthermia. 62 5
17356545 2007
8
A new type of congenital disorders of glycosylation (CDG-Ii) provides new insights into the early steps of dolichol-linked oligosaccharide biosynthesis. 62 5
12684507 2003
9
ATP6AP1-CDG: Follow-up and female phenotype. 57
32395412 2020
10
TMEM199 Deficiency Is a Disorder of Golgi Homeostasis Characterized by Elevated Aminotransferases, Alkaline Phosphatase, and Cholesterol and Abnormal Glycosylation. 5
26833330 2016
11
CCDC115 Deficiency Causes a Disorder of Golgi Homeostasis with Abnormal Protein Glycosylation. 5
26833332 2016
12
A new mutation in COG7 extends the spectrum of COG subunit deficiencies. 5
19577670 2009
13
Molecular and clinical characterization of a Moroccan Cog7 deficient patient. 5
17395513 2007
14
Mutation of the COG complex subunit gene COG7 causes a lethal congenital disorder. 5
15107842 2004
15
Synergistic use of glycomics and single-molecule molecular inversion probes for identification of congenital disorders of glycosylation type-1. 62
35279850 2022
16
Infant Robot-assisted Laparoscopic Pyeloplasty: Outcomes at a Single Institution, and Tips for Safety and Success. 62
34247895 2021
17
MAN1B1-CDG: novel patients and novel variant. 62
34162022 2021
18
SLC35A2-CDG: novel variants with two ends of the spectrum. 62
34161696 2021
19
A patient-based medaka alg2 mutant as a model for hypo-N-glycosylation. 62
34106226 2021
20
SLC37A4-CDG: Second patient. 62
33728255 2021
21
Development and Initial Characterization of Cellular Models for COG Complex-Related CDG-II Diseases. 62
34603392 2021
22
Liver failure and x-linked immunodeficiency type 47. 62
32790950 2020
23
Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry to Detect Diagnostic Glycopeptide Markers of Congenital Disorders of Glycosylation. 62
32547898 2020
24
Relative quantification of plasma N-glycans in type II congenital disorder of glycosylation patients by mass spectrometry. 62
30776362 2019
25
Clinical and molecular diagnosis of non-phosphomannomutase 2 N-linked congenital disorders of glycosylation in Spain. 62
30653653 2019
26
Ten years of screening for congenital disorders of glycosylation in Argentina: case studies and pitfalls. 62
30397276 2018
27
Use of Endoglycosidase H as a diagnostic tool for MAN1B1-CDG patients. 62
29947113 2018
28
More than just sugars: Conserved oligomeric Golgi complex deficiency causes glycosylation-independent cellular defects. 62
29573151 2018
29
Functional analysis of SLC39A8 mutations and their implications for manganese deficiency and mitochondrial disorders. 62
29453449 2018
30
Modeling Congenital Disorders of N-Linked Glycoprotein Glycosylation in Drosophila melanogaster. 62
30333856 2018
31
An Unexplained Congenital Disorder of Glycosylation-II in a Child with Neurohepatic Involvement, Hypercholesterolemia and Hypoceruloplasminemia. 62
28643274 2018
32
COG7 deficiency in Drosophila generates multifaceted developmental, behavioral and protein glycosylation phenotypes. 62
28883096 2017
33
TMEM165 deficiencies in Congenital Disorders of Glycosylation type II (CDG-II): Clues and evidences for roles of the protein in Golgi functions and ion homeostasis. 62
27401145 2017
34
Phenotypic and genotypic spectrum of congenital disorders of glycosylation type I and type II. 62
28122681 2017
35
Classification of congenital disorders of glycosylation based on analysis of transferrin glycopeptides by capillary liquid chromatography-mass spectrometry. 62
27591658 2016
36
Global serum glycoform profiling for the investigation of dystroglycanopathies & Congenital Disorders of Glycosylation. 62
27134828 2016
37
COG Complex Complexities: Detailed Characterization of a Complete Set of HEK293T Cells Lacking Individual COG Subunits. 62
27066481 2016
38
High-resolution mass spectrometry glycoprofiling of intact transferrin for diagnosis and subtype identification in the congenital disorders of glycosylation. 62
26307094 2015
39
Genetic defects in dolichol metabolism. 62
25270028 2015
40
Congenital disorders of glycosylation with emphasis on cerebellar involvement. 62
25192513 2014
41
Diagnostic serum glycosylation profile in patients with intellectual disability as a result of MAN1B1 deficiency. 62
24566669 2014
42
Wrinkled skin and fat pads in patients with ALG8-CDG: revisiting skin manifestations in congenital disorders of glycosylation. 62
24555185 2014
43
Impact of disease-causing mutations on TMEM165 subcellular localization, a recently identified protein involved in CDG-II. 62
23575229 2013
44
A novel congenital disorder of glycosylation type without central nervous system involvement caused by mutations in the phosphoglucomutase 1 gene. 62
22976764 2013
45
Roles of the nucleotide sugar transporters (SLC35 family) in health and disease. 62
23506892 2013
46
Perinatal and early infantile symptoms in congenital disorders of glycosylation. 62
23401092 2013
47
Approaches to homozygosity mapping and exome sequencing for the identification of novel types of CDG. 62
22983704 2013
48
MAN1B1 deficiency: an unexpected CDG-II. 62
24348268 2013
49
COG5-CDG: expanding the clinical spectrum. 62
23228021 2012
50
TMEM165 deficiency causes a congenital disorder of glycosylation. 62
22683087 2012

Variations for Immunodeficiency 47

ClinVar genetic disease variations for Immunodeficiency 47:

5 (show top 50) (show all 407)
# Gene Name Type Significance ClinVarId dbSNP ID Position
1 CCDC115 NM_032357.4(CCDC115):c.31G>T (p.Asp11Tyr) SNV Pathogenic
218963 rs869025583 GRCh37: 2:131099668-131099668
GRCh38: 2:130342095-130342095
2 TMEM199 NM_152464.3(TMEM199):c.40G>C (p.Ala14Pro) SNV Pathogenic
223000 rs869025586 GRCh37: 17:26684733-26684733
GRCh38: 17:28357710-28357710
3 TMEM199 NM_152464.3(TMEM199):c.92G>C (p.Arg31Pro) SNV Pathogenic
218964 rs782531869 GRCh37: 17:26684785-26684785
GRCh38: 17:28357762-28357762
4 CCDC115 NM_032357.4(CCDC115):c.92T>C (p.Leu31Ser) SNV Pathogenic
Pathogenic
218967 rs751325113 GRCh37: 2:131099607-131099607
GRCh38: 2:130342034-130342034
5 TMEM199 NM_152464.3(TMEM199):c.20C>A (p.Ala7Glu) SNV Pathogenic
218965 rs369488804 GRCh37: 17:26684713-26684713
GRCh38: 17:28357690-28357690
6 ATP6AP1 NM_001183.6(ATP6AP1):c.1284G>A (p.Met428Ile) SNV Pathogenic
236239 rs878853275 GRCh37: X:153664108-153664108
GRCh38: X:154435762-154435762
7 ATP6AP1 NM_001183.6(ATP6AP1):c.938A>G (p.Tyr313Cys) SNV Pathogenic
236242 rs878853278 GRCh37: X:153663499-153663499
GRCh38: X:154435153-154435153
8 ATP6AP1 NM_001183.6(ATP6AP1):c.431T>C (p.Leu144Pro) SNV Pathogenic
236240 rs878853276 GRCh37: X:153660679-153660679
GRCh38: X:154432333-154432333
9 ATP6AP1 NM_001183.6(ATP6AP1):c.542T>G (p.Leu181Arg) SNV Pathogenic
437913 rs1557196978 GRCh37: X:153660790-153660790
GRCh38: X:154432444-154432444
10 ATP6AP1 NM_001183.6(ATP6AP1):c.221T>C (p.Leu74Pro) SNV Pathogenic
915879 rs2068680774 GRCh37: X:153657453-153657453
GRCh38: X:154429107-154429107
11 ATP6AP1 NM_001183.6(ATP6AP1):c.932T>A (p.Leu311Gln) SNV Pathogenic
804234 rs1603384499 GRCh37: X:153663493-153663493
GRCh38: X:154435147-154435147
12 ATP6AP1 NM_001183.6(ATP6AP1):c.649T>A (p.Tyr217Asn) SNV Pathogenic
973847 rs2068705545 GRCh37: X:153662031-153662031
GRCh38: X:154433685-154433685
13 ALG2 NM_033087.4(ALG2):c.752G>T (p.Arg251Leu) SNV Pathogenic
1676197 GRCh37: 9:101980715-101980715
GRCh38: 9:99218433-99218433
14 COG7 NM_153603.4(COG7):c.169+4A>C SNV Pathogenic
3650 rs1555497568 GRCh37: 16:23464143-23464143
GRCh38: 16:23452822-23452822
15 overlap with 117 genes DEL Pathogenic
1684654 GRCh37:
GRCh38: X:153427468-156004919
16 COG7 NM_153603.4(COG7):c.1476-1G>T SNV Pathogenic
548708 rs1555493029 GRCh37: 16:23417584-23417584
GRCh38: 16:23406263-23406263
17 COG7 NM_153603.4(COG7):c.1A>G (p.Met1Val) SNV Pathogenic
1334892 GRCh37: 16:23464315-23464315
GRCh38: 16:23452994-23452994
18 COG7 NM_153603.4(COG7):c.170-7A>G SNV Pathogenic
3651 rs1555496968 GRCh37: 16:23457289-23457289
GRCh38: 16:23445968-23445968
19 CEP290 NM_025114.4(CEP290):c.5668G>T (p.Gly1890Ter) SNV Pathogenic
1333 rs137852832 GRCh37: 12:88471040-88471040
GRCh38: 12:88077263-88077263
20 ALG2 NM_033087.4(ALG2):c.1040del (p.Gly347fs) DEL Pathogenic
Likely Pathogenic
2699 rs387906281 GRCh37: 9:101980427-101980427
GRCh38: 9:99218145-99218145
21 ALG2 NM_033087.4(ALG2):c.393G>T (p.Lys131Asn) SNV Pathogenic
2700 rs730880304 GRCh37: 9:101981074-101981074
GRCh38: 9:99218792-99218792
22 ALG2 NM_033087.4(ALG2):c.176G>A (p.Cys59Tyr) SNV Likely Pathogenic
1184506 GRCh37: 9:101984001-101984001
GRCh38: 9:99221719-99221719
23 ALG2 NM_033087.4(ALG2):c.89_114del (p.Glu30fs) DEL Likely Pathogenic
Uncertain Significance
1035954 rs775204090 GRCh37: 9:101984063-101984088
GRCh38: 9:99221781-99221806
24 COG7 NM_153603.4(COG7):c.1817C>A (p.Ala606Asp) SNV Likely Pathogenic
1184979 GRCh37: 16:23409437-23409437
GRCh38: 16:23398116-23398116
25 COG7 NM_153603.4(COG7):c.1046A>G (p.Asp349Gly) SNV Likely Pathogenic
1184980 GRCh37: 16:23430112-23430112
GRCh38: 16:23418791-23418791
26 COG7 NM_153603.4(COG7):c.2T>C (p.Met1Thr) SNV Likely Pathogenic
548709 rs1555497604 GRCh37: 16:23464314-23464314
GRCh38: 16:23452993-23452993
27 ATP6AP1 NM_001183.6(ATP6AP1):c.230_232del (p.Tyr77del) DEL Likely Pathogenic
1686802 GRCh37: X:153657460-153657462
GRCh38: X:154429114-154429116
28 ATP6AP1 NM_001183.6(ATP6AP1):c.1036G>A (p.Glu346Lys) SNV Likely Pathogenic
236241 rs878853277 GRCh37: X:153663684-153663684
GRCh38: X:154435338-154435338
29 ALG2 NM_033087.4(ALG2):c.218_225del (p.Asp73fs) DEL Likely Pathogenic
915335 rs1828806280 GRCh37: 9:101983952-101983959
GRCh38: 9:99221670-99221677
30 COG7 NM_153603.4(COG7):c.319-12C>T SNV Conflicting Interpretations Of Pathogenicity
518138 rs201965984 GRCh37: 16:23456497-23456497
GRCh38: 16:23445176-23445176
31 COG7 NM_153603.4(COG7):c.1305T>C (p.Asp435=) SNV Conflicting Interpretations Of Pathogenicity
884915 rs1019861391 GRCh37: 16:23424873-23424873
GRCh38: 16:23413552-23413552
32 COG7 NM_153603.4(COG7):c.75C>G (p.Ser25=) SNV Conflicting Interpretations Of Pathogenicity
318495 rs149481813 GRCh37: 16:23464241-23464241
GRCh38: 16:23452920-23452920
33 COG7 NM_153603.4(COG7):c.904G>A (p.Val302Met) SNV Conflicting Interpretations Of Pathogenicity
724610 rs116314856 GRCh37: 16:23436175-23436175
GRCh38: 16:23424854-23424854
34 COG7 NM_153603.4(COG7):c.170-4A>G SNV Conflicting Interpretations Of Pathogenicity
318491 rs544015151 GRCh37: 16:23457286-23457286
GRCh38: 16:23445965-23445965
35 COG7 NM_153603.4(COG7):c.963C>T (p.Thr321=) SNV Conflicting Interpretations Of Pathogenicity
318480 rs762510375 GRCh37: 16:23436116-23436116
GRCh38: 16:23424795-23424795
36 COG7 NM_153603.4(COG7):c.900C>T (p.Asn300=) SNV Conflicting Interpretations Of Pathogenicity
318481 rs112611398 GRCh37: 16:23436179-23436179
GRCh38: 16:23424858-23424858
37 COG7 NM_153603.4(COG7):c.1137+11A>C SNV Conflicting Interpretations Of Pathogenicity
318478 rs74012174 GRCh37: 16:23430010-23430010
GRCh38: 16:23418689-23418689
38 ALG2 NM_033087.4(ALG2):c.475A>G (p.Ile159Val) SNV Conflicting Interpretations Of Pathogenicity
390397 rs146770430 GRCh37: 9:101980992-101980992
GRCh38: 9:99218710-99218710
39 COG7 NM_153603.4(COG7):c.1972G>A (p.Ala658Thr) SNV Conflicting Interpretations Of Pathogenicity
772628 rs115073082 GRCh37: 16:23404584-23404584
GRCh38: 16:23393263-23393263
40 COG7 NM_153603.4(COG7):c.1178A>G (p.His393Arg) SNV Conflicting Interpretations Of Pathogenicity
318477 rs116331296 GRCh37: 16:23428402-23428402
GRCh38: 16:23417081-23417081
41 COG7 NM_153603.4(COG7):c.1971C>T (p.His657=) SNV Conflicting Interpretations Of Pathogenicity
318465 rs114458562 GRCh37: 16:23404585-23404585
GRCh38: 16:23393264-23393264
42 COG7 NM_153603.4(COG7):c.2052G>A (p.Ser684=) SNV Conflicting Interpretations Of Pathogenicity
318463 rs142744907 GRCh37: 16:23403795-23403795
GRCh38: 16:23392474-23392474
43 COG7 NM_153603.4(COG7):c.2283C>T (p.Thr761=) SNV Conflicting Interpretations Of Pathogenicity
194800 rs144814374 GRCh37: 16:23400271-23400271
GRCh38: 16:23388950-23388950
44 COG7 NM_153603.4(COG7):c.435+2T>C SNV Conflicting Interpretations Of Pathogenicity
657072 rs201446992 GRCh37: 16:23456367-23456367
GRCh38: 16:23445046-23445046
45 COG7 NM_153603.4(COG7):c.1113C>T (p.Leu371=) SNV Conflicting Interpretations Of Pathogenicity
697694 rs114661874 GRCh37: 16:23430045-23430045
GRCh38: 16:23418724-23418724
46 COG7 NM_153603.4(COG7):c.1455C>T (p.Phe485=) SNV Conflicting Interpretations Of Pathogenicity
318472 rs116153163 GRCh37: 16:23421636-23421636
GRCh38: 16:23410315-23410315
47 COG7 NM_153603.4(COG7):c.1405A>G (p.Ile469Val) SNV Uncertain Significance
318475 rs751036976 GRCh37: 16:23424773-23424773
GRCh38: 16:23413452-23413452
48 COG7 NM_153603.4(COG7):c.2297G>A (p.Arg766Gln) SNV Uncertain Significance
538565 rs368136642 GRCh37: 16:23400257-23400257
GRCh38: 16:23388936-23388936
49 ALG2 NM_033087.4(ALG2):c.232G>C (p.Gly78Arg) SNV Uncertain Significance
657644 rs1054683823 GRCh37: 9:101983945-101983945
GRCh38: 9:99221663-99221663
50 ALG2 NM_033087.4(ALG2):c.784G>T (p.Val262Phe) SNV Uncertain Significance
660985 rs1229029511 GRCh37: 9:101980683-101980683
GRCh38: 9:99218401-99218401

UniProtKB/Swiss-Prot genetic disease variations for Immunodeficiency 47:

73
# Symbol AA change Variation ID SNP ID
1 ATP6AP1 p.Leu144Pro VAR_077021 rs878853276
2 ATP6AP1 p.Tyr313Cys VAR_077022 rs878853278
3 ATP6AP1 p.Glu346Lys VAR_077023 rs878853277
4 ATP6AP1 p.Met428Ile VAR_077024 rs878853275

Expression for Immunodeficiency 47

Search GEO for disease gene expression data for Immunodeficiency 47.

Pathways for Immunodeficiency 47



Pathways related to Immunodeficiency 47 according to GeneCards Suite gene sharing:

# Super pathways Score Top Affiliating Genes
1
Show member pathways
13.63 SRD5A3 SLC35C1 SLC35A1 MPI MAN1B1 COG7
2
Show member pathways
13.54 SRD5A3 SLC35C1 SLC35A1 PGM1 MPI MAN1B1
3
Show member pathways
12.61 SRD5A3 SLC35C1 SLC35A1 MPI MAN1B1 COG7
4
Show member pathways
12.56 ALG1 ALG2 ALG6 ALG8 B4GALT1 MAN1B1
5
Show member pathways
12.08 SRD5A3 SLC35C1 SLC35A1 MPI ALG8 ALG6

GO Terms for Immunodeficiency 47

Cellular components related to Immunodeficiency 47 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 membrane GO:0016020 10.81 ALG1 ALG2 ALG6 ALG8 ATP6AP1 ATP6V0A2
2 membrane GO:0016021 10.81 ALG1 ALG2 ALG6 ALG8 ATP6AP1 ATP6V0A2
3 endoplasmic reticulum GO:0005783 10.22 TMEM199 SRD5A3 MAN1B1 CCDC115 ATP6AP1 ALG8
4 endoplasmic reticulum membrane GO:0005789 10.06 ALG1 ALG2 ALG6 ALG8 ATP6AP1 MAN1B1
5 Golgi membrane GO:0000139 9.8 TMEM165 SLC35C1 SLC35A1 COG7 COG1 B4GALT1
6 proton-transporting V-type ATPase complex GO:0033176 9.67 ATP6V0A2 ATP6AP1
7 Golgi transport complex GO:0017119 9.62 COG7 COG1
8 vacuolar proton-transporting V-type ATPase complex GO:0016471 9.1 TMEM199 CCDC115 ATP6V0A2

Biological processes related to Immunodeficiency 47 according to GeneCards Suite gene sharing:

(show all 14)
# Name GO ID Score Top Affiliating Genes
1 carbohydrate metabolic process GO:0005975 10.02 B4GALT1 MAN1B1 MPI PGM1 SLC35A1
2 cellular iron ion homeostasis GO:0006879 9.97 ATP6AP1 ATP6V0A2 CCDC115 TMEM199
3 lysosomal lumen acidification GO:0007042 9.93 TMEM199 CCDC115 ATP6AP1
4 protein N-linked glycosylation GO:0006487 9.92 TMEM165 B4GALT1 ALG8 ALG6
5 glycosylation GO:0070085 9.91 COG7 COG1 B4GALT1
6 mannosylation GO:0097502 9.88 ALG8 ALG2 ALG1
7 Golgi lumen acidification GO:0061795 9.84 ATP6V0A2 ATP6AP1
8 retrograde transport, vesicle recycling within Golgi GO:0000301 9.83 COG7 COG1
9 lysosomal protein catabolic process GO:1905146 9.81 TMEM199 CCDC115
10 vacuolar proton-transporting V-type ATPase complex assembly GO:0070072 9.8 TMEM199 CCDC115
11 cellular response to increased oxygen levels GO:0036295 9.76 ATP6AP1 ATP6V0A2 CCDC115 TMEM199
12 oligosaccharide-lipid intermediate biosynthetic process GO:0006490 9.73 ALG8 ALG6 ALG2
13 dolichol-linked oligosaccharide biosynthetic process GO:0006488 9.65 SRD5A3 ALG8 ALG6 ALG2 ALG1
14 protein glycosylation GO:0006486 9.4 SRD5A3 MAN1B1 COG7 B4GALT1 ALG8 ALG6

Molecular functions related to Immunodeficiency 47 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 alpha-1,3-mannosyltransferase activity GO:0000033 9.46 ALG8 ALG2
2 dolichyl-phosphate-glucose-glycolipid alpha-glucosyltransferase activity GO:0004583 9.26 ALG8 ALG6
3 glycosyltransferase activity GO:0016757 9.02 B4GALT1 ALG8 ALG6 ALG2 ALG1

Sources for Immunodeficiency 47

2 CDC
6 CNVD
8 Cosmic
9 dbSNP
10 DGIdb
16 EFO
17 ExPASy
18 FMA
19 GARD
27 GO
28 GTR
29 HMDB
30 HPO
31 ICD10
32 ICD10 via Orphanet
33 ICD11
34 ICD9CM
35 IUPHAR
36 LifeMap
38 LOVD
40 MedGen
43 MeSH
44 MESH via Orphanet
45 MGI
48 NCI
49 NCIt
50 NDF-RT
52 NINDS
53 Novoseek
55 ODiseA
56 OMIM via Orphanet
57 OMIM® (Updated 08-Dec-2022)
61 PubChem
62 PubMed
64 QIAGEN
69 SNOMED-CT via HPO
70 Tocris
71 UMLS
72 UMLS via Orphanet
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