MSeqDR Mitochondrial disease browser phenotype pathogenic gene and mutation portal

About
MSeqDR-LSDB
Tools
- Quick-Mitome for WES
- Quick-Mitome
- Quick-Mitome Report
- mtDNA Tool:
- mvTool
- Phy-Mer
- MToolBox
- mvTool for Haplogroup
- mvTool with HmtDB
- MitoMaster
- MitoTIP tRNA Scoring
- MSeq-OpenCGA
- Variant Tool:
- VariantOneStop
- HBCR Exome (Retired)
- POLG Patho. Server
- Data - Awsomics GeEx
- Expert Panel
- Panel Tool:
- Gene Panel Examiner
- Transgenomic_NuclearMitome
- Pedigree Maker
- json2table
Phenome-Disease
Collaboration
- Genesis (GEM.App)
- LeighMap
- Expert Panel
- Collaboration Zone
Submission
- Submit_Interpret_Variant
- Instructions

Hello! Guest! Please Login or Register! Clinician Mode

Examples Gene: MT-ND1, POLG, Region: M:1-1000 Variant: m.8993T>G, 1:g.10042757T>C rs3888511 MSCV_0000006, ClinVar: RCV000000015, Disease: Leigh syndrome, Phenotype: Retinopathy

MSeqDR Mitochondrial Disease Portal

*:HP: HPO terms, UMDF: 1= Disease, ND: NAMDC terms.
Most Studied CPEO, Complex I Deficiency, COXPD1, Leigh, LHON, MELAS, MERRF, Myopathy, SANDO

Disease Browser
Parent Node: Immunologic Deficiency Syndromes (D007153)
..Starting node ..IMMUNODEFICIENCY 47 (OMIM:300972)
Child Nodes:
Sister Nodes:
..Activated PI3K-delta Syndrome (C585640)
..Agammaglobulinemia (D000361) 19
..Antibody Deficiency due to Defect in CD19 (C566275)
..Ataxia Telangiectasia (D001260) 6
..AUTOINFLAMMATION, ANTIBODY DEFICIENCY, AND IMMUNE DYSREGULATION, PLCG2-ASSOCIATED (OMIM:614878)
..B-Cell Immunodeficiency, Distal Limb Anomalies, And Urogenital Malformations (C563745)
..C1q DEFICIENCY (OMIM:613652)
..C9 Deficiency (C565165)
..C9 Deficiency with Dermatomyositis (C565166)
..Cartilage hair hypoplasia like syndrome (C535915)
..Cartilage-hair hypoplasia (C535916)
..Cd4+ Lymphocyte Deficiency (C566079)
..CD8 Deficiency, Familial (C563824)
..Combined Immunodeficiency with Autoimmunity and Spondylometaphyseal Dysplasia (C564307)
..Combined Inflammatory and Immunologic Defect (C565684)
..Common Variable Immunodeficiency (D017074)
..COMPLEMENT COMPONENT 2 DEFICIENCY (OMIM:217000)
..Complement Component 3 Deficiency, Autosomal Recessive (C565169)
..Complement Component 4, Partial Deficiency Of (C565168)
..Complement Component 4a Deficiency (C565167)
..COMPLEMENT COMPONENT 4B DEFICIENCY (OMIM:614379)
..Complement component 5 deficiency (C537005)
..Complement Component 6 Deficiency (C567307)
..Complement Component 7 Deficiency (C566443)
..COMPLEMENT COMPONENT C1r/C1s DEFICIENCY (OMIM:216950)
..Complement Component C1s Deficiency (C565170)
..COMPLEMENT FACTOR B DEFICIENCY (OMIM:615561)
..Complement Factor D Deficiency (C565027)
..Davenport Donlan syndrome (C535988)
..Deltaretrovirus Infections (D006800) 4
..Diarrhea, Glucose-Stimulated Secretory, with Common Variable Immunodeficiency (C565099)
..Dysgammaglobulinemia (D004406) 11
..Ectodermal Dysplasia, Anhidrotic, with Immunodeficiency, Osteopetrosis, and Lymphedema (C564538)
..Ectodermal Dysplasia, Anhidrotic, With T-Cell Immunodeficiency, Autosomal Dominant (C567411)
..Ectodermal dysplasia, hypohidrotic, with immune deficiency (C536181)
..Endotoxin Hyporesponsiveness (C566417)
..Enteropathy, Familial, with Villous Edema and Immunoglobulin G2 Deficiency (C563949)
..ERYTHRODERMA, CONGENITAL, WITH PALMOPLANTAR KERATODERMA, HYPOTRICHOSIS, AND HYPER-IgE (OMIM:615508)
..FACIAL DYSMORPHISM, IMMUNODEFICIENCY, LIVEDO, AND SHORT STATURE (OMIM:615139)
..Fanconi like syndrome (C536855)
..FICOLIN 3 DEFICIENCY (OMIM:613860)
..Griscelli syndrome type 2 (C537302)
..Hepatic venoocclusive disease with immunodeficiency (C537257)
..HIV Infections (D015658) 12
..Hypoglobulinemia and Absent B Cells (C565765)
..Immune Deficiency Disease (C565469)
..Immune Deficiency, Familial Variable (C564136)
..IMMUNODEFICIENCY 11 (OMIM:615206)
..IMMUNODEFICIENCY 12 (OMIM:615468)
..IMMUNODEFICIENCY 14 (OMIM:615513)
..IMMUNODEFICIENCY 15B (OMIM:615592)
..IMMUNODEFICIENCY 16 (OMIM:615593)
..IMMUNODEFICIENCY 17 (OMIM:615607)
..IMMUNODEFICIENCY 18 (OMIM:615615)
..IMMUNODEFICIENCY 19 (OMIM:615617)
..IMMUNODEFICIENCY 20 (OMIM:615707)
..IMMUNODEFICIENCY 21 (OMIM:614172)
..IMMUNODEFICIENCY 22 (OMIM:615758)
..IMMUNODEFICIENCY 23 (OMIM:615816)
..IMMUNODEFICIENCY 24 (OMIM:615897)
..IMMUNODEFICIENCY 26 WITH OR WITHOUT NEUROLOGIC ABNORMALITIES (OMIM:615966)
..IMMUNODEFICIENCY 27B (OMIM:615978)
..IMMUNODEFICIENCY 28 (OMIM:614889)
..IMMUNODEFICIENCY 29 (OMIM:614890)
..IMMUNODEFICIENCY 30 (OMIM:614891)
..IMMUNODEFICIENCY 31A (OMIM:614892)
..IMMUNODEFICIENCY 31B (OMIM:613796)
..IMMUNODEFICIENCY 31C (OMIM:614162)
..IMMUNODEFICIENCY 32A (OMIM:614893)
..IMMUNODEFICIENCY 32B (OMIM:226990)
..IMMUNODEFICIENCY 36 (OMIM:616005)
..IMMUNODEFICIENCY 37 (OMIM:616098)
..IMMUNODEFICIENCY 38 WITH BASAL GANGLIA CALCIFICATION (OMIM:616126)
..IMMUNODEFICIENCY 39 (OMIM:616345)
..IMMUNODEFICIENCY 40 (OMIM:616433)
..IMMUNODEFICIENCY 42 (OMIM:616622)
..IMMUNODEFICIENCY 44 (OMIM:616636)
..IMMUNODEFICIENCY 45 (OMIM:616669)
..IMMUNODEFICIENCY 46 (OMIM:616740)
..IMMUNODEFICIENCY 47 (OMIM:300972)
..IMMUNODEFICIENCY 48 (OMIM:269840)
..IMMUNODEFICIENCY 49 (OMIM:617237)
..IMMUNODEFICIENCY 50 (OMIM:300988)
..IMMUNODEFICIENCY 51 (OMIM:613953)
..IMMUNODEFICIENCY 54 (OMIM:609981)
..IMMUNODEFICIENCY 56 (OMIM:615207)
..IMMUNODEFICIENCY 8 (OMIM:615401)
..Immunodeficiency due to Defect in CD3-Epsilon (C566082)
..Immunodeficiency due to Defect in CD3-Gamma (C566083)
..Immunodeficiency due to Defect in CD3-Zeta (C565712)
..Immunodeficiency due to Defect in MAPBP-Interacting Protein (C563663)
..Immunodeficiency syndrome, variable (C537362) 1
..Immunodeficiency with Defective Leukocyte and Lymphocyte Function and with Response to Histamine-1 Antagonist (C564135)
..Immunodeficiency without anhidrotic ectodermal dysplasia (C536289)
..Immunodeficiency, Gonadal Dysgenesis, And Pulmonary Fibrosis (C567457)
..Immunodeficiency, Hypogammaglobulinemia, and Reduced B Cells (C567200)
..Immunodeficiency, Partial Combined, with Absence of HLA Determinants and Beta-2-Microglobulin from Lymphocytes (C565468)
..Immunodeficiency, X-Linked, with Deficiency of 115,000 Dalton Surface Glycoprotein (C564120)
..IMMUNOGLOBULIN KAPPA LIGHT CHAIN DEFICIENCY (OMIM:614102)
..Inosine Phosphorylase Deficiency, Immune Defect Due To (C565465)
..Interleukin 2 Receptor, Alpha, Deficiency of (C565232)
..Invasive Pneumococcal Disease, Recurrent Isolated, 1 (C563662)
..Invasive Pneumococcal Disease, Recurrent Isolated, 2 (C564468)
..IRAK4 Deficiency (C564352)
..Kappa-Chain Deficiency (C564131)
..Kotzot-Richter syndrome (C537025)
..Leukocyte-Adhesion Deficiency Syndrome (D018370) 2
..Lichtenstein syndrome (C535894)
..LIG4 Syndrome (C564694)
..LUNG DISEASE, IMMUNODEFICIENCY, AND CHROMOSOME BREAKAGE SYNDROME (OMIM:617241)
..Lymphoblastic Transformation, Intrinsic Defect in (C565431)
..Lymphoid System Deterioration, Progressive (C565430)
..Lymphokine Deficiency (C565428)
..Lymphopenia (D008231) 5
..Lymphopenic Hypergammaglobulinemia, Antibody Deficiency, Autoimmune Hemolytic Anemia, and Glomerulonephritis (C565427)
..MASP2 Deficiency (C565360)
..MYD88 Deficiency (C567379)
..Myelodysplasia, Immunodeficiency, Facial Dysmorphism, Short Stature, and Psychomotor Delay (C563345)
..Natural Killer Cell Deficiency, Familial Isolated (C566492)
..NEMO mutation with immunodeficiency (C538399)
..Neutrophil Immunodeficiency Syndrome (C564275)
..Phagocyte Bactericidal Dysfunction (D010585) 14
..Properdin Deficiency, Type II (C564075)
..Properdin Deficiency, Type III (C564076)
..Riddle Syndrome (C567453)
..Roifman syndrome (C535866)
..Roifman-Chitayat Syndrome (C567641)
..Schimke immunoosseous dysplasia (C536629)
..Severe Combined Immunodeficiency (D016511) 22 C:1
..Severe Combined Immunodeficiency, Autosomal Recessive, T Cell-Negative, B Cell-Negative, NK Cell-Positive (C563311)
..Splenic Hypoplasia (C563028)
..T cell immunodeficiency primary (C536780)
..T-CELL IMMUNODEFICIENCY, RECURRENT INFECTIONS, AND AUTOIMMUNITY WITH OR WITHOUT CARDIAC MALFORMATIONS (OMIM:614868)
..T-Cell OKT4 Deficiency (C566080)
..T-CELL RECEPTOR-ALPHA/BETA DEFICIENCY (OMIM:615387)
..Thumb Agenesis, Short Stature, And Immunodeficiency (C564770)
..Thymic aplasia (C536288)
..Tuftsin Deficiency (C562872)
..WHIM syndrome (C536697)
Human Disease MESH is developed by UMLS. Further data from MedGen, OMIM,ClinVar, CTD

Term ID:

6282

Name:

IMMUNODEFICIENCY 47

Definition:

Alternative IDs:

ParentIDs:

MESH:D007153

TreeNumbers:

C20.673/300972

Synonyms:

IMD47 |IMMUNODEFICIENCY AND HEPATOPATHY WITH OR WITHOUT NEUROLOGIC FEATURES

Slim Mappings:

Immune system disease

Reference:

MedGen: 300972
MeSH: 300972
OMIM: 300972;
MSeqDR :
Genes:

Phenotypes

1	HP:0001419	X-linked recessive inheritance
2	HP:0001394	Cirrhosis NAMDC: Cirrhosis
3	HP:0004313	Decreased antibody level in blood
4	HP:0002910	Elevated hepatic transaminases
5	HP:0001397	Hepatic steatosis NAMDC: Hepatopathy with steatosis or oncocytic changes by liver biopsy
6	HP:0002240	Hepatomegaly
7	HP:0000540	Hypermetropia
8	HP:0001249	Intellectual disability	HP:0040283
9	HP:0001882	Leukopenia
10	HP:0006579	Prolonged neonatal jaundice
11	HP:0002718	Recurrent bacterial infections
12	HP:0001250	Seizures NAMDC: Seizures	HP:0040283
13	HP:0000407	Sensorineural hearing impairment NAMDC: Sensorineural hearing loss
14	HP:0001744	Splenomegaly
15	HP:0003828	Variable expressivity

Disease Causing ClinVar Variants

Variation_Name	GeneID	GeneSymbol	ClinicalSignificance	dbSNP	RCVaccession	TestedInGTR	PhenotypeIDs	Chromosome	Start	Stop	HGVS_g	OtherIDs	Disease_ClinVar
NM_001183.6(ATP6AP1):c.216G>A (p.Leu72=)	537	ATP6AP1	Conflicting interpretations of pathogenicity	-1	RCV002590148\|RCV003146587;	N	MedGen:CN517202\|MONDO:MONDO:0010504,MedGen:C4310819,OMIM:300972	X	153657448	153657448		-
NM_001183.6(ATP6AP1):c.220C>G (p.Leu74Val)	537	ATP6AP1	Conflicting interpretations of pathogenicity	-1	RCV003312786\|RCV003330115;	N	MedGen:C3661900\|MONDO:MONDO:0010504,MedGen:C4310819,OMIM:300972	X	153657452	153657452		-
NM_001183.6(ATP6AP1):c.221T>C (p.Leu74Pro)	537	ATP6AP1	Pathogenic	2068680774	RCV001171364;	N	MONDO:MONDO:0010504,MedGen:C4310819,OMIM:300972	X	153657453	153657453	X:g.153657453T>C	OMIM:300197.0006
NM_001183.6(ATP6AP1):c.230_232del (p.Tyr77del)	537	ATP6AP1	Likely pathogenic	2148221946	RCV002248303;	N	MONDO:MONDO:0010504,MedGen:C4310819,OMIM:300972	X	153657460	153657462	153657459	-
NM_001183.6(ATP6AP1):c.289-135=	537	ATP6AP1	Benign	11156577	RCV000843501\|RCV001553938;	N	MedGen:C3661900\|MONDO:MONDO:0010504,MedGen:C4310819,OMIM:300972	X	153660041	153660041	X:g.153660041C>T	-
NM_001183.6(ATP6AP1):c.301G>A (p.Asp101Asn)	537	ATP6AP1	Uncertain significance	-1	RCV003143651;	N	MONDO:MONDO:0010504,MedGen:C4310819,OMIM:300972	X	153660188	153660188	NC_000023.10:g.153660188G>A	-
NM_001183.6(ATP6AP1):c.385T>C (p.Ser129Pro)	537	ATP6AP1	Uncertain significance	-1	RCV003152911;	N	MONDO:MONDO:0010504,MedGen:C4310819,OMIM:300972	X	153660633	153660633		-
NM_001183.6(ATP6AP1):c.431T>C (p.Leu144Pro)	537	ATP6AP1	Pathogenic	878853276	RCV000225250;	N	MONDO:MONDO:0010504,MedGen:C4310819,OMIM:300972	X	153660679	153660679	X:g.153660679T>C	ClinGen:CA10581575,UniProtKB:Q15904#VAR_077021,OMIM:300197.0002	C3151226 613860 Immunodeficiency due to ficolin 3 deficiency;
NM_001183.6(ATP6AP1):c.473A>T (p.His158Leu)	537	ATP6AP1	Uncertain significance	-1	RCV003340895;	N	MONDO:MONDO:0010504,MedGen:C4310819,OMIM:300972	X	153660721	153660721		-
NM_001183.6(ATP6AP1):c.515G>C (p.Ser172Thr)	537	ATP6AP1	Uncertain significance	-1	RCV003143652;	N	MONDO:MONDO:0010504,MedGen:C4310819,OMIM:300972	X	153660763	153660763	NC_000023.10:g.153660763G>C	-
NM_001183.6(ATP6AP1):c.530T>C (p.Leu177Pro)	537	ATP6AP1	Likely pathogenic	-1	RCV003149154;	N	MONDO:MONDO:0010504,MedGen:C4310819,OMIM:300972	X	153660778	153660778		-
NM_001183.6(ATP6AP1):c.542T>G (p.Leu181Arg)	537	ATP6AP1	Conflicting interpretations of pathogenicity	1557196978	RCV000590996\|RCV001857199;	N	MONDO:MONDO:0010504,MedGen:C4310819,OMIM:300972\|MedGen:CN517202	X	153660790	153660790	X:g.153660790T>G	ClinGen:CA415190062,OMIM:300197.0005	C4310819 300972 Immunodeficiency 47;
NM_001183.6(ATP6AP1):c.560C>T (p.Ser187Phe)	537	ATP6AP1	Uncertain significance	-1	RCV003329096;	N	MONDO:MONDO:0010504,MedGen:C4310819,OMIM:300972	X	153661279	153661279		-
NM_001183.6(ATP6AP1):c.649T>A (p.Tyr217Asn)	537	ATP6AP1	Pathogenic	2068705545	RCV001250487;	N	MONDO:MONDO:0010504,MedGen:C4310819,OMIM:300972	X	153662031	153662031	X:g.153662031T>A	OMIM:300197.0008
NM_001183.6(ATP6AP1):c.674G>A (p.Arg225His)	537	ATP6AP1	Uncertain significance	782349780	RCV001195771;	N	MONDO:MONDO:0010504,MedGen:C4310819,OMIM:300972	X	153662056	153662056	X:g.153662056G>A	-
NM_001183.6(ATP6AP1):c.932T>A (p.Leu311Gln)	537	ATP6AP1	Conflicting interpretations of pathogenicity	1603384499	RCV000991196\|RCV001171365;	N	\|MONDO:MONDO:0010504,MedGen:C4310819,OMIM:300972	X	153663493	153663493	X:g.153663493T>A	OMIM:300197.0007
NM_001183.6(ATP6AP1):c.938A>G (p.Tyr313Cys)	537	ATP6AP1	Pathogenic	878853278	RCV000225189\|RCV003238745;	N	MONDO:MONDO:0010504,MedGen:C4310819,OMIM:300972\|MedGen:CN517202	X	153663499	153663499	X:g.153663499A>G	ClinGen:CA10581577,UniProtKB:Q15904#VAR_077022,OMIM:300197.0004	C3151226 613860 Immunodeficiency due to ficolin 3 deficiency;
NM_001183.6(ATP6AP1):c.971+10G>A	537	ATP6AP1	Conflicting interpretations of pathogenicity	-1	RCV002843740\|RCV003225772;	N	MedGen:C3661900\|MONDO:MONDO:0010504,MedGen:C4310819,OMIM:300972	X	153663542	153663542	NC_000023.10:g.153663542G>A	-
NM_001183.6(ATP6AP1):c.1031G>A (p.Arg344His)	537	ATP6AP1	Uncertain significance	781936333	RCV001823571\|RCV002542733\|RCV002545194;	N	MONDO:MONDO:0010504,MedGen:C4310819,OMIM:300972\|MeSH:D030342,MedGen:C0950123\|MedGen:C3661900	X	153663679	153663679	153663679	-
NM_001183.6(ATP6AP1):c.1036G>A (p.Glu346Lys)	537	ATP6AP1	Pathogenic/Likely pathogenic	878853277	RCV000225332\|RCV001560673;	N	MONDO:MONDO:0010504,MedGen:C4310819,OMIM:300972\|MedGen:CN517202	X	153663684	153663684	NC_000023.10:g.153663684G>A	ClinGen:CA10581576,UniProtKB:Q15904#VAR_077023,OMIM:300197.0003	C3151226 613860 Immunodeficiency due to ficolin 3 deficiency;
NM_001183.6(ATP6AP1):c.1284G>A (p.Met428Ile)	537	ATP6AP1	Pathogenic	878853275	RCV000225137;	N	MONDO:MONDO:0010504,MedGen:C4310819,OMIM:300972	X	153664108	153664108	X:g.153664108G>A	UniProtKB:Q15904#VAR_077024,OMIM:300197.0001,ClinGen:CA10581574	C3151226 613860 Immunodeficiency due to ficolin 3 deficiency;

MSeqDR Portal

Feedback about the webpages , or email to MSeqDR webmaster: Lishuang Shen