IMD47
MCID: IMM140
MIFTS: 56

Immunodeficiency 47 (IMD47)

Categories: Cardiovascular diseases, Eye diseases, Fetal diseases, Genetic diseases, Immune diseases, Infectious diseases, Liver diseases, Metabolic diseases, Neuronal diseases, Rare diseases, Skin diseases

Aliases & Classifications for Immunodeficiency 47

MalaCards integrated aliases for Immunodeficiency 47:

Name: Immunodeficiency 47 57 12 72 29 6 15
Congenital Disorder of Glycosylation Type Ii 12 58 72 15 17
Congenital Disorder of Glycosylation Type Iie 12 58 72 15
Cdg2e 57 12 58 72
Immunodeficiency and Hepatopathy with or Without Neurologic Features 57 12 72
Congenital Disorder of Glycosylation, Type Iie 57 13 6
Congenital Disorder of Glycosylation, Type Ii 57 13 70
Congenital Disorder of Glycosylation Type 2e 58 44 70
Alg2-Cdg 58 29 6
Cdg Iis 57 12 72
Cdg Iie 57 12 72
Cdgiis 57 12 72
Imd47 57 12 72
Cdg2s 57 12 72
Cdg1i 57 58 72
Carbohydrate Deficient Glycoprotein Syndrome Type Iie 12 58
Congenital Disorder of Glycosylation, Type Iis 57 72
Congenital Disorders of Glycosylation Type Ii 36 6
Congenital Disorder of Glycosylation Ii 12 15
Congenital Disorder of Glycosylation 1i 12 72
Cdg Syndrome Type Iie 12 58
Cdg-Iie 58 72
Cdg Ii 57 72
Cdgiie 57 72
Cdg-Ii 58 72
Cdgii 57 72
Congenital Disorder of Glycosylation, Type Iis; Cdg2s 57
Carbohydrate Deficient Glycoprotein Syndrome Type Ii 58
Glycosylation, Congenital Disorder of, Type Iie 39
Glycosylation, Congenital Disorder of, Type Ii 39
Congenital Disorder of Glycosylation Type Iis 12
Congenital Disorder of Glycosylation Type 2a 70
Congenital Disorder of Glycosylation Type 1i 58
Congenital Disorder of Glycosylation 2e 72
Congenital Disorder of Glycosylation 2s 72
Mannosyltransferase 2 Deficiency 58
Immunodeficiency, Type 47 39
Cdg Syndrome Type Ii 58
Cdg Iis; Cdgiis 57
Cdg Iie; Cdgiie 57
Cdg Ii; Cdgii 57
Cog7-Cdg 58
Cdgiide 12

Characteristics:

Orphanet epidemiological data:

58
cog7-cdg
Inheritance: Autosomal recessive; Prevalence: <1/1000000 (Worldwide); Age of onset: Infancy,Neonatal; Age of death: early childhood;
alg2-cdg
Inheritance: Autosomal recessive; Prevalence: <1/1000000 (Worldwide); Age of onset: Infancy,Neonatal;

OMIM®:

57 (Updated 05-Apr-2021)
Miscellaneous:
variable severity

Inheritance:
x-linked recessive


HPO:

31
congenital disorder of glycosylation, type ii:
Inheritance autosomal recessive inheritance

congenital disorder of glycosylation, type iie:
Inheritance autosomal recessive inheritance

immunodeficiency 47:
Onset and clinical course variable expressivity
Inheritance x-linked recessive inheritance


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


Summaries for Immunodeficiency 47

UniProtKB/Swiss-Prot : 72 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.
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.

MalaCards based summary : Immunodeficiency 47, also known as congenital disorder of glycosylation type ii, is related to congenital disorder of glycosylation, type iig and congenital disorder of glycosylation, type iij, and has symptoms including seizures An important gene associated with Immunodeficiency 47 is ALG2 (ALG2 Alpha-1,3/1,6-Mannosyltransferase), and among its related pathways/superpathways are N-Glycan biosynthesis and Metabolism. Affiliated tissues include eye, liver and heart, and related phenotypes are nystagmus and cataract

Disease Ontology : 12 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.

OMIM® : 57 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). (300972) (Updated 05-Apr-2021)

KEGG : 36 Congenital disorders of glycosylation (CDG) are a group of disorders caused by defects in various genes for N-glycan biosynthesis. CDG-II is defined by mutations in genes encoding enzymes in the processing of N-glycans on the glycosylated proteins either late in the endoplasmic reticulum or the Golgi compartments. Multiple subtypes have been identified although the numbers and forms of affected individuals with CDG-I are still much more. In contrast to type I, the type II patients show a more severe psychomotor retardation, no peripheral neuropathy and a cerebellar hypoplasia. According to the serum transferrin glycoform, a portion of CDG-II can be diagnosed. Distinct from CDG-I, the serum trisialo- and asialotransferrin are increased in CDG-II.

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 54)
# Related Disease Score Top Affiliating Genes
1 congenital disorder of glycosylation, type iig 32.5 COG1 ALG2
2 congenital disorder of glycosylation, type iij 32.4 COG1 ALG2
3 congenital disorder of glycosylation, type iil 32.4 COG7 COG1
4 congenital disorder of glycosylation, type iih 32.3 COG7 COG1 ALG8 ALG6 ALG2
5 congenital disorder of glycosylation, type iim 32.3 SLC35A1 MAN1B1 B4GALT1 ALG2 ALG1
6 congenital disorder of glycosylation, type iin 32.2 PMM2 DPM1
7 congenital disorder of glycosylation, type iio 32.2 TMEM199 MAN1B1 CCDC115 ATP6V0A2 ATP6AP1 ALG8
8 congenital disorder of glycosylation, type iip 32.2 TMEM199 MAN1B1 CCDC115 ATP6V0A2 ATP6AP1 ALG8
9 congenital disorder of glycosylation, type iib 32.1 SLC35C1 SLC35A1 MPI MAN1B1 B4GALT1 ALG2
10 congenital disorder of glycosylation, type iia 32.1 SLC35C1 SLC35A1 PMM2 MPI B4GALT1 ALG2
11 congenital disorder of glycosylation, type ic 32.1 PMM2 ALG6
12 congenital disorder of glycosylation, type iid 32.0 SLC35C1 SLC35A1 PMM2 MPI COG7 COG1
13 congenital disorder of glycosylation, type iii 32.0 DPM1 COG7 COG1 B4GALT1 ALG8 ALG6
14 congenital disorder of glycosylation, type iif 31.9 SLC35C1 SLC35A1 MPI MAN1B1 COG1 B4GALT1
15 congenital disorder of glycosylation, type iik 31.9 TMEM165 SLC35C1 MAN1B1 DOLK COG1 ATP6V0A2
16 congenital disorders of n-linked glycosylation and multiple pathway 30.5 B4GALT1 ALG8 ALG6 ALG2 ALG1
17 congenital disorder of glycosylation, type in 29.2 TMEM199 TMEM165 SLC35C1 SLC35A1 PMM2 MPI
18 man1b1-cdg 11.5
19 congenital disorder of glycosylation, type iic 11.2
20 congenital disorder of glycosylation, type iiq 11.2
21 congenital disorder of glycosylation, type ih 10.4 ALG8 ALG2
22 myopathy, x-linked, with excessive autophagy 10.4 TMEM199 CCDC115 ATP6AP1
23 congenital muscular dystrophy-dystroglycanopathy type a2 10.4 ALG6 ALG2
24 autosomal recessive cutis laxa type ii classic type 10.4 COG7 CCDC115 ATP6V0A2
25 geroderma osteodysplasticum 10.4 COG7 ATP6V0A2 ALG2
26 fructose intolerance, hereditary 10.3 SLC35C1 MAN1B1 B4GALT1 ALG2
27 autosomal recessive disease 10.3
28 peripheral nervous system disease 10.3
29 neuropathy 10.3
30 congenital disorder of glycosylation, type im 10.3 DPM1 DOLK
31 protein-losing enteropathy 10.2 PMM2 MPI ALG8 ALG6
32 galactosemia i 10.2 TMEM165 PMM2 COG7 B4GALT1 ALG2
33 kahrizi syndrome 10.2 DPM1 DOLK
34 cone-rod dystrophy, x-linked, 1 10.2 COG7 COG1
35 cerebellar hypoplasia 10.2
36 congenital dyserythropoietic anemia 10.2
37 congenital disorder of glycosylation, type ie 10.1 SLC35C1 SLC35A1 PMM2 DPM1 DOLK ALG6
38 hypotonia 10.1
39 schneckenbecken dysplasia 10.1 SLC35C1 SLC35A1
40 triiodothyronine receptor auxiliary protein 10.1
41 hypercholesterolemia, familial, 1 10.0
42 aceruloplasminemia 10.0
43 walker-warburg syndrome 10.0 SLC35A1 PMM2 MPI DPM1 DOLK ATP6V0A2
44 congenital disorder of glycosylation, type i/iix 9.9
45 immune deficiency disease 9.9
46 bilirubin metabolic disorder 9.9
47 liver disease 9.9
48 47,xyy 9.9
49 coloboma of macula 9.8
50 rafiq syndrome 9.8

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 31 (show top 50) (show all 73)
# Description HPO Frequency Orphanet Frequency HPO Source Accession
1 nystagmus 58 31 hallmark (90%) Very frequent (99-80%) HP:0000639
2 cataract 58 31 hallmark (90%) Very frequent (99-80%) HP:0000518
3 cognitive impairment 58 31 hallmark (90%) Very frequent (99-80%) HP:0100543
4 hypertrophic cardiomyopathy 58 31 hallmark (90%) Very frequent (99-80%) HP:0001639
5 abnormality of immune system physiology 58 31 hallmark (90%) Very frequent (99-80%) HP:0010978
6 iris coloboma 58 31 hallmark (90%) Very frequent (99-80%) HP:0000612
7 seizure 31 occasional (7.5%) HP:0001250
8 hypotonia 31 hallmark (90%) HP:0001252
9 intellectual disability 31 occasional (7.5%) HP:0001249
10 seizures 58 Very frequent (99-80%)
11 hyperreflexia 31 HP:0001347
12 failure to thrive 31 HP:0001508
13 short neck 31 HP:0000470
14 muscular hypotonia 58 Very frequent (99-80%)
15 respiratory insufficiency 31 HP:0002093
16 hearing impairment 31 HP:0000365
17 global developmental delay 31 HP:0001263
18 splenomegaly 31 HP:0001744
19 hepatomegaly 31 HP:0002240
20 abnormal facial shape 31 HP:0001999
21 short nose 31 HP:0003196
22 thick vermilion border 31 HP:0012471
23 smooth philtrum 31 HP:0000319
24 sensorineural hearing impairment 31 HP:0000407
25 visual impairment 31 HP:0000505
26 short stature 31 HP:0004322
27 gastroesophageal reflux 31 HP:0002020
28 hypoglycemia 31 HP:0001943
29 skeletal muscle atrophy 31 HP:0003202
30 congestive heart failure 31 HP:0001635
31 intrauterine growth retardation 31 HP:0001511
32 retrognathia 31 HP:0000278
33 micrognathia 31 HP:0000347
34 low-set ears 31 HP:0000369
35 hepatic steatosis 31 HP:0001397
36 elevated hepatic transaminase 31 HP:0002910
37 inverted nipples 31 HP:0003186
38 cirrhosis 31 HP:0001394
39 elevated serum creatine kinase 31 HP:0003236
40 jaundice 31 HP:0000952
41 narrow mouth 31 HP:0000160
42 upslanted palpebral fissure 31 HP:0000582
43 protruding tongue 31 HP:0010808
44 hydronephrosis 31 HP:0000126
45 low anterior hairline 31 HP:0000294
46 adducted thumb 31 HP:0001181
47 hyporeflexia 31 HP:0001265
48 abnormality of coagulation 31 HP:0001928
49 profound global developmental delay 31 HP:0012736
50 wide nose 31 HP:0000445

Symptoms via clinical synopsis from OMIM®:

57 (Updated 05-Apr-2021)
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
cirrhosis
fibrosis
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 05-Apr-2021)

UMLS symptoms related to Immunodeficiency 47:


seizures

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

26
# Description GenomeRNAi Source Accession Score Top Affiliating Genes
1 Decreased viability GR00240-S-1 9.4 COG7
2 Decreased viability GR00249-S 9.4 ALG2 B4GALT1 SLC35C1
3 Decreased viability GR00381-A-1 9.4 B4GALT1
4 Decreased viability GR00386-A-1 9.4 ALG1 ALG6 COG7 MPI TMEM165
5 Decreased viability GR00402-S-2 9.4 ATP6V0A2 TMEM165
6 Decreased shRNA abundance GR00297-A 9.26 ALG1 DOLK MPI PMM2

MGI Mouse Phenotypes related to Immunodeficiency 47:

46
# Description MGI Source Accession Score Top Affiliating Genes
1 mortality/aging MP:0010768 9.44 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 2e

Genetic Tests for Immunodeficiency 47

Genetic tests related to Immunodeficiency 47:

# Genetic test Affiliating Genes
1 Alg2-Cdg 29 ALG2
2 Immunodeficiency 47 29 ATP6AP1

Anatomical Context for Immunodeficiency 47

MalaCards organs/tissues related to Immunodeficiency 47:

40
Eye, Liver, Heart, Skeletal Muscle, Tongue

Publications for Immunodeficiency 47

Articles related to Immunodeficiency 47:

(show all 21)
# 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. 6 57
32216104 2020
2
Prenatal and postnatal phenotype of a pathologic variant in the ATP6AP1 gene. 57 6
32058063 2020
3
Expanding the phenotype of metabolic cutis laxa with an additional disorder of N-linked protein glycosylation. 6 57
29192153 2018
4
Cutis laxa, exocrine pancreatic insufficiency and altered cellular metabolomics as additional symptoms in a new patient with ATP6AP1-CDG. 57 6
29396028 2018
5
ATP6AP1 deficiency causes an immunodeficiency with hepatopathy, cognitive impairment and abnormal protein glycosylation. 6 57
27231034 2016
6
ATP6AP1-CDG: Follow-up and female phenotype. 57
32395412 2020
7
CCDC115 Deficiency Causes a Disorder of Golgi Homeostasis with Abnormal Protein Glycosylation. 6
26833332 2016
8
TMEM199 Deficiency Is a Disorder of Golgi Homeostasis Characterized by Elevated Aminotransferases, Alkaline Phosphatase, and Cholesterol and Abnormal Glycosylation. 6
26833330 2016
9
Targeted polymerase chain reaction-based enrichment and next generation sequencing for diagnostic testing of congenital disorders of glycosylation. 6
21811164 2011
10
A new mutation in COG7 extends the spectrum of COG subunit deficiencies. 6
19577670 2009
11
Molecular and clinical characterization of a Moroccan Cog7 deficient patient. 6
17395513 2007
12
A common mutation in the COG7 gene with a consistent phenotype including microcephaly, adducted thumbs, growth retardation, VSD and episodes of hyperthermia. 6
17356545 2007
13
Mutation of the COG complex subunit gene COG7 causes a lethal congenital disorder. 6
15107842 2004
14
A new type of congenital disorders of glycosylation (CDG-Ii) provides new insights into the early steps of dolichol-linked oligosaccharide biosynthesis. 6
12684507 2003
15
SLC37A4-CDG: Second patient. 61
33728255 2021
16
Functional analysis of SLC39A8 mutations and their implications for manganese deficiency and mitochondrial disorders. 61
29453449 2018
17
Diagnostic serum glycosylation profile in patients with intellectual disability as a result of MAN1B1 deficiency. 61
24566669 2014
18
Golgi function and dysfunction in the first COG4-deficient CDG type II patient. 61
19494034 2009
19
A rapid mass spectrometric strategy for the characterization of N- and O-glycan chains in the diagnosis of defects in glycan biosynthesis. 61
17520685 2007
20
A new inborn error of glycosylation due to a Cog8 deficiency reveals a critical role for the Cog1-Cog8 interaction in COG complex formation. 61
17220172 2007
21
Conserved oligomeric Golgi complex subunit 1 deficiency reveals a previously uncharacterized congenital disorder of glycosylation type II. 61
16537452 2006

Variations for Immunodeficiency 47

ClinVar genetic disease variations for Immunodeficiency 47:

6 (show top 50) (show all 207)
# Gene Name Type Significance ClinVarId dbSNP ID Position
1 COG7 NM_153603.4(COG7):c.169+4A>C SNV Pathogenic 3650 rs1555497568 GRCh37: 16:23464143-23464143
GRCh38: 16:23452822-23452822
2 COG7 NM_153603.4(COG7):c.1476-1G>T SNV Pathogenic 548708 rs1555493029 GRCh37: 16:23417584-23417584
GRCh38: 16:23406263-23406263
3 ALG2 NM_033087.4(ALG2):c.1040del (p.Gly347fs) Deletion Pathogenic 2699 rs387906281 GRCh37: 9:101980427-101980427
GRCh38: 9:99218145-99218145
4 ALG2 NM_033087.4(ALG2):c.393G>T (p.Lys131Asn) SNV Pathogenic 2700 rs730880304 GRCh37: 9:101981074-101981074
GRCh38: 9:99218792-99218792
5 CCDC115 NM_032357.4(CCDC115):c.31G>T (p.Asp11Tyr) SNV Pathogenic 218963 rs869025583 GRCh37: 2:131099668-131099668
GRCh38: 2:130342095-130342095
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.1036G>A (p.Glu346Lys) SNV Pathogenic 236241 rs878853277 GRCh37: X:153663684-153663684
GRCh38: X:154435338-154435338
10 ATP6AP1 NM_001183.6(ATP6AP1):c.221T>C (p.Leu74Pro) SNV Pathogenic 915879 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 TMEM199 NM_152464.3(TMEM199):c.20C>A (p.Ala7Glu) SNV Pathogenic 218965 rs369488804 GRCh37: 17:26684713-26684713
GRCh38: 17:28357690-28357690
13 TMEM199 NM_152464.3(TMEM199):c.92G>C (p.Arg31Pro) SNV Pathogenic 218964 rs782531869 GRCh37: 17:26684785-26684785
GRCh38: 17:28357762-28357762
14 TMEM199 NM_152464.3(TMEM199):c.40G>C (p.Ala14Pro) SNV Pathogenic 223000 rs869025586 GRCh37: 17:26684733-26684733
GRCh38: 17:28357710-28357710
15 ATP6AP1 NM_001183.6(ATP6AP1):c.649T>A (p.Tyr217Asn) SNV Pathogenic 973847 GRCh37: X:153662031-153662031
GRCh38: X:154433685-154433685
16 COG7 NM_153603.4(COG7):c.170-7A>G SNV Pathogenic 3651 rs1555496968 GRCh37: 16:23457289-23457289
GRCh38: 16:23445968-23445968
17 CCDC115 NM_032357.4(CCDC115):c.92T>C (p.Leu31Ser) SNV Pathogenic 218967 rs751325113 GRCh37: 2:131099607-131099607
GRCh38: 2:130342034-130342034
18 CCDC115 NM_032357.4(CCDC115):c.92T>C (p.Leu31Ser) SNV Pathogenic 218967 rs751325113 GRCh37: 2:131099607-131099607
GRCh38: 2:130342034-130342034
19 ATP6AP1 NM_001183.6(ATP6AP1):c.542T>G (p.Leu181Arg) SNV Pathogenic 437913 rs1557196978 GRCh37: X:153660790-153660790
GRCh38: X:154432444-154432444
20 COG7 NM_153603.4(COG7):c.2118_2121dup (p.Ala708fs) Microsatellite Pathogenic 1032506 GRCh37: 16:23403725-23403726
GRCh38: 16:23392404-23392405
21 ALG2 NM_033087.4(ALG2):c.1040del (p.Gly347fs) Deletion Likely pathogenic 2699 rs387906281 GRCh37: 9:101980427-101980427
GRCh38: 9:99218145-99218145
22 ALG2 NM_033087.4(ALG2):c.218_225del (p.Asp73fs) Deletion Likely pathogenic 915335 GRCh37: 9:101983952-101983959
GRCh38: 9:99221670-99221677
23 COG7 NM_153603.4(COG7):c.2T>C (p.Met1Thr) SNV Likely pathogenic 548709 rs1555497604 GRCh37: 16:23464314-23464314
GRCh38: 16:23452993-23452993
24 COG7 NM_153603.4(COG7):c.435+2T>C SNV Likely pathogenic 657072 rs201446992 GRCh37: 16:23456367-23456367
GRCh38: 16:23445046-23445046
25 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
26 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
27 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
28 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
29 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
30 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
31 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
32 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
33 COG7 NM_153603.4(COG7):c.754G>A (p.Gly252Arg) SNV Uncertain significance 938128 GRCh37: 16:23444922-23444922
GRCh38: 16:23433601-23433601
34 COG7 NM_153603.4(COG7):c.1388C>T (p.Thr463Met) SNV Uncertain significance 499717 rs764153683 GRCh37: 16:23424790-23424790
GRCh38: 16:23413469-23413469
35 ALG2 NM_033087.4(ALG2):c.215G>T (p.Gly72Val) SNV Uncertain significance 941497 GRCh37: 9:101983962-101983962
GRCh38: 9:99221680-99221680
36 ALG2 NM_033087.4(ALG2):c.1150G>A (p.Ala384Thr) SNV Uncertain significance 947697 GRCh37: 9:101980317-101980317
GRCh38: 9:99218035-99218035
37 ALG2 NM_033087.4(ALG2):c.388C>T (p.Arg130Trp) SNV Uncertain significance 967908 GRCh37: 9:101981079-101981079
GRCh38: 9:99218797-99218797
38 COG7 NM_153603.4(COG7):c.86C>T (p.Ala29Val) SNV Uncertain significance 318494 rs146918812 GRCh37: 16:23464230-23464230
GRCh38: 16:23452909-23452909
39 ALG2 NM_033087.4(ALG2):c.1132C>T (p.Arg378Cys) SNV Uncertain significance 265036 rs56393253 GRCh37: 9:101980335-101980335
GRCh38: 9:99218053-99218053
40 ALG2 NM_033087.4(ALG2):c.449T>C (p.Phe150Ser) SNV Uncertain significance 575832 rs377047079 GRCh37: 9:101981018-101981018
GRCh38: 9:99218736-99218736
41 COG7 NM_153603.4(COG7):c.1717C>T (p.Arg573Trp) SNV Uncertain significance 318469 rs548129734 GRCh37: 16:23415101-23415101
GRCh38: 16:23403780-23403780
42 COG7 NM_153603.4(COG7):c.818A>G (p.Gln273Arg) SNV Uncertain significance 1032507 GRCh37: 16:23436261-23436261
GRCh38: 16:23424940-23424940
43 ALG2 NM_033087.4(ALG2):c.89_114del (p.Glu30fs) Deletion Uncertain significance 1035954 GRCh37: 9:101984063-101984088
GRCh38: 9:99221781-99221806
44 ALG2 NM_033087.4(ALG2):c.1218G>C (p.Gln406His) SNV Uncertain significance 1039238 GRCh37: 9:101980249-101980249
GRCh38: 9:99217967-99217967
45 ALG2 NM_033087.4(ALG2):c.945C>T (p.Cys315=) SNV Uncertain significance 1041171 GRCh37: 9:101980522-101980522
GRCh38: 9:99218240-99218240
46 ALG2 NM_033087.4(ALG2):c.367G>A (p.Val123Met) SNV Uncertain significance 1041393 GRCh37: 9:101981100-101981100
GRCh38: 9:99218818-99218818
47 COG7 NM_153603.4(COG7):c.2281A>G (p.Thr761Ala) SNV Uncertain significance 1045814 GRCh37: 16:23400273-23400273
GRCh38: 16:23388952-23388952
48 ALG2 NM_033087.4(ALG2):c.434C>T (p.Thr145Ile) SNV Uncertain significance 1047589 GRCh37: 9:101981033-101981033
GRCh38: 9:99218751-99218751
49 ALG2 NM_033087.4(ALG2):c.449T>C (p.Phe150Ser) SNV Uncertain significance 575832 rs377047079 GRCh37: 9:101981018-101981018
GRCh38: 9:99218736-99218736
50 COG7 NM_153603.4(COG7):c.109G>A (p.Ala37Thr) SNV Uncertain significance 449289 rs1327432623 GRCh37: 16:23464207-23464207
GRCh38: 16:23452886-23452886

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

72
# 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 KEGG:

36
# Name Kegg Source Accession
1 N-Glycan biosynthesis hsa00510

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

# Super pathways Score Top Affiliating Genes
1
Show member pathways
13.79 PMM2 MPI MAN1B1 DPM1 DOLK B4GALT1
2
Show member pathways
13.53 SLC35C1 SLC35A1 PMM2 MPI MAN1B1 DPM1
3
Show member pathways
12.36 SLC35C1 SLC35A1 PMM2 MPI MAN1B1 DPM1
4
Show member pathways
11.94 SLC35C1 SLC35A1 PMM2 MPI DPM1 DOLK
5
Show member pathways
11.76 MAN1B1 DPM1 DOLK B4GALT1 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 10.19 TMEM199 TMEM165 SLC35C1 SLC35A1 MAN1B1 DPM1
2 integral component of membrane GO:0016021 10.18 TMEM199 TMEM165 SLC35C1 SLC35A1 MAN1B1 DOLK
3 Golgi apparatus GO:0005794 9.95 TMEM165 SLC35C1 SLC35A1 MAN1B1 COG7 COG1
4 endoplasmic reticulum GO:0005783 9.81 TMEM199 MAN1B1 DPM1 DOLK CCDC115 ATP6AP1
5 Golgi membrane GO:0000139 9.8 TMEM165 SLC35C1 SLC35A1 COG7 COG1 B4GALT1
6 trans-Golgi network membrane GO:0032588 9.61 TMEM165 COG7 COG1
7 Golgi transport complex GO:0017119 9.46 COG7 COG1
8 endoplasmic reticulum membrane GO:0005789 9.28 TMEM199 MAN1B1 DPM1 DOLK ATP6AP1 ALG8
9 vacuolar proton-transporting V-type ATPase complex GO:0016471 9.13 TMEM199 CCDC115 ATP6V0A2

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

(show all 13)
# Name GO ID Score Top Affiliating Genes
1 carbohydrate metabolic process GO:0005975 9.81 SLC35A1 MPI MAN1B1 B4GALT1
2 cellular iron ion homeostasis GO:0006879 9.71 TMEM199 CCDC115 ATP6V0A2 ATP6AP1
3 mannosylation GO:0097502 9.62 DPM1 ALG8 ALG2 ALG1
4 dolichol-linked oligosaccharide biosynthetic process GO:0006488 9.56 ALG8 ALG6 ALG2 ALG1
5 protein N-linked glycosylation GO:0006487 9.55 TMEM165 PMM2 B4GALT1 ALG8 ALG6
6 oligosaccharide-lipid intermediate biosynthetic process GO:0006490 9.54 ALG8 ALG6 ALG2
7 protein N-linked glycosylation via asparagine GO:0018279 9.52 DPM1 ALG8
8 lysosomal lumen acidification GO:0007042 9.49 TMEM199 CCDC115
9 lysosomal protein catabolic process GO:1905146 9.48 TMEM199 CCDC115
10 vacuolar proton-transporting V-type ATPase complex assembly GO:0070072 9.46 TMEM199 CCDC115
11 GDP-mannose biosynthetic process GO:0009298 9.43 PMM2 MPI
12 protein glycosylation GO:0006486 9.32 PMM2 MPI MAN1B1 DPM1 COG7 B4GALT1
13 cellular response to increased oxygen levels GO:0036295 9.26 TMEM199 CCDC115 ATP6V0A2 ATP6AP1

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

# Name GO ID Score Top Affiliating Genes
1 transferase activity, transferring hexosyl groups GO:0016758 9.26 ALG8 ALG6
2 alpha-1,3-mannosyltransferase activity GO:0000033 9.16 ALG8 ALG2
3 transferase activity, transferring glycosyl groups GO:0016757 9.1 DPM1 B4GALT1 ALG8 ALG6 ALG2 ALG1
4 dolichyl-phosphate-glucose-glycolipid alpha-glucosyltransferase activity GO:0004583 8.96 ALG8 ALG6

Sources for Immunodeficiency 47

3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
17 EFO
18 ExPASy
19 FMA
20 GARD
28 GO
29 GTR
30 HMDB
31 HPO
32 ICD10
33 ICD10 via Orphanet
34 ICD9CM
35 IUPHAR
36 KEGG
37 LifeMap
39 LOVD
41 MedGen
44 MeSH
45 MESH via Orphanet
46 MGI
49 NCI
50 NCIt
51 NDF-RT
53 NINDS
54 Novoseek
56 OMIM via Orphanet
57 OMIM® (Updated 05-Apr-2021)
61 PubMed
63 QIAGEN
68 SNOMED-CT via HPO
69 Tocris
70 UMLS
71 UMLS via Orphanet
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