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	alpha-1-antitrypsin deficiency

Disease ID	21
Disease	alpha-1-antitrypsin deficiency
Definition	autosomal recessive trait leading to destruction of lung tissue by neutrophil elastase and eventual emphysema; second only to cystic fibrosis as most common lethal genetic disorder among Caucasians of northern European ancestry.
Synonym	1 alpha antitrypsin deficiency a-1atd a1ad a1atd aat deficiency aatd alpha 1 antitrypsin defic alpha 1 antitrypsin deficiency alpha 1-antitrypsin deficiencies alpha 1-antitrypsin deficiency alpha 1-antitrypsin deficiency [disease/finding] alpha antitrypsin deficiency 01 alpha-1 anti-trypsin deficiency alpha-1 antitrypsin deficiency alpha-1-antitrypsin def alpha-1-antitrypsin deficiency (disorder) alpha-1-proteinase inhibitor deficiency deficiencies, alpha 1-antitrypsin deficiency, alpha 1-antitrypsin
Orphanet	ORPHANET:60
OMIM	OMIM:613490
DOID	DOID:13372
ICD10	ICD10CM:E88.01
UMLS	C0221757
MeSH	D019896
SNOMED-CT	SNOMEDCT_US_2016_09_01:30188007
Comorbidity	UMLS \| Disease \| Sentences' Count(Total Sentences:30) C0013990 \| emphysema \| 15 C0221757 \| alpha-1 antitrypsin deficiency \| 7 C0024115 \| lung disease \| 6 C0023895 \| liver disease \| 6 C0030326 \| panniculitis \| 4 C0006267 \| bronchiectasis \| 3 C0600260 \| obstructive pulmonary disease \| 3 C0024115 \| pulmonary disease \| 3 C0221757 \| alpha 1-antitrypsin deficiency \| 3 C0024117 \| chronic obstructive pulmonary disease \| 3 C0282193 \| iron overload \| 2 C0022353 \| neonatal jaundice \| 2 C0024115 \| lung diseases \| 2 C0023890 \| cirrhosis \| 2 C0034067 \| pulmonary emphysema \| 2 C0032285 \| pulmonary inflammation \| 1 C0006272 \| bronchiolitis obliterans \| 1 C0004096 \| bronchial asthma \| 1 C0003864 \| arthritis \| 1 C0023890 \| liver cirrhosis \| 1 C0004096 \| asthma \| 1 C0032326 \| pneumothorax \| 1 C0016053 \| fibromyalgia \| 1 C0024117 \| chronic obstructive pulmonary disease (copd) \| 1 C0242379 \| lung cancer \| 1 C0019158 \| hepatitis \| 1 C0034065 \| pulmonary embolus \| 1 C0035204 \| respiratory disease \| 1 C0042384 \| vasculitis \| 1 C0019163 \| hepatitis b \| 1
Curated Gene	Entrez_id \| Symbol \| Resource(Total Genes:1) 5265 \| SERPINA1 \| CLINVAR;CTD_human;GHR;ORPHANET;UNIPROT
Inferring Gene	Entrez_id \| Symbol \| Resource(Total Genes:2) 3123 \| HLA-DRB1 \| CIPHER 5265 \| SERPINA1 \| CIPHER;CTD_human
Text Mined Gene	Entrez_id \| Symbol \| Score \| Resource(Total Genes:44) 2 \| A2M \| 2.975 \| DISEASES 34 \| ACADM \| 1.32 \| DISEASES 174 \| AFP \| 1.734 \| DISEASES 229 \| ALDOB \| 2.583 \| DISEASES 22926 \| ATF6 \| 1.773 \| DISEASES 8678 \| BECN1 \| 1.043 \| DISEASES 1769 \| DNAH8 \| 2.701 \| DISEASES 954 \| ENTPD2 \| 1.406 \| DISEASES 26232 \| FBXO2 \| 2.223 \| DISEASES 2266 \| FGG \| 1.327 \| DISEASES 2638 \| GC \| 2.237 \| DISEASES 728441 \| GGT2 \| 1.643 \| DISEASES 84706 \| GPT2 \| 1.292 \| DISEASES 2950 \| GSTP1 \| 1.334 \| DISEASES 9709 \| HERPUD1 \| 1.681 \| DISEASES 3077 \| HFE \| 2.552 \| DISEASES 57608 \| KIAA1462 \| 2.595 \| DISEASES 3875 \| KRT18 \| 1.197 \| DISEASES 3988 \| LIPA \| 1.668 \| DISEASES 11253 \| MAN1B1 \| 2.589 \| DISEASES 5005 \| ORM2 \| 1.821 \| DISEASES 80235 \| PIGZ \| 3.266 \| DISEASES 5292 \| PIM1 \| 4.725 \| DISEASES 11040 \| PIM2 \| 1.324 \| DISEASES 415116 \| PIM3 \| 2.174 \| DISEASES 6014 \| RIT2 \| 1.291 \| DISEASES 5265 \| SERPINA1 \| 8.313 \| DISEASES 12 \| SERPINA3 \| 4.17 \| DISEASES 5104 \| SERPINA5 \| 1.197 \| DISEASES 866 \| SERPINA6 \| 1.645 \| DISEASES 1992 \| SERPINB1 \| 3.96 \| DISEASES 462 \| SERPINC1 \| 2.373 \| DISEASES 5270 \| SERPINE2 \| 2.268 \| DISEASES 6439 \| SFTPB \| 1.496 \| DISEASES 83733 \| SLC25A18 \| 1.403 \| DISEASES 6590 \| SLPI \| 3.106 \| DISEASES 345079 \| SOWAHB \| 3.324 \| DISEASES 258010 \| SVIP \| 2.87 \| DISEASES 84447 \| SYVN1 \| 2.165 \| DISEASES 117145 \| THEM4 \| 1.09 \| DISEASES 51643 \| TMBIM4 \| 4.684 \| DISEASES 8718 \| TNFRSF25 \| 1.306 \| DISEASES 83696 \| TRAPPC9 \| 1.652 \| DISEASES 7415 \| VCP \| 1.031 \| DISEASES
Locus	Symbol \| Locus(Total Locus:1) SERPINA1 \| 14q32.13

Disease ID	21
Disease	alpha-1-antitrypsin deficiency
Integrated Phenotype	HPO \| Name(Total Integrated Phenotypes:6) HP:0001399 \| Hepatic failure HP:0002097 \| Emphysema HP:0000100 \| Nephrotic syndrome HP:0012115 \| Hepatitis HP:0002240 \| Hepatomegaly HP:0000952 \| Jaundice
Text Mined Phenotype	HPO \| Name \| Sentences' Count(Total Phenotypes:23) HP:0002097 \| Pulmonary emphysema \| 18 HP:0012490 \| Inflammation of fat tissue \| 4 HP:0002110 \| Bronchiectasis \| 3 HP:0006510 \| Chronic obstructive pulmonary disease \| 3 HP:0001394 \| Hepatic cirrhosis \| 2 HP:0000952 \| Yellow skin \| 2 HP:0006579 \| Neonatal jaundice \| 2 HP:0200123 \| Chronic liver inflammation \| 2 HP:0002647 \| Aortic dissection \| 1 HP:0002107 \| Collapsed lung \| 1 HP:0002617 \| Aneurysmal dilatation \| 1 HP:0004313 \| Decreased immunoglobulin level \| 1 HP:0012050 \| Anasarca \| 1 HP:0002094 \| Dyspnea \| 1 HP:0001373 \| Joint dislocations \| 1 HP:0002633 \| Vasculitis \| 1 HP:0002099 \| Asthma \| 1 HP:0012115 \| Liver inflammation \| 1 HP:0001369 \| Arthritis \| 1 HP:0002108 \| Spontaneous pneumothorax \| 1 HP:0006509 \| Tracheal diverticulum \| 1 HP:0011946 \| Constrictive bronchiolitis \| 1 HP:0001907 \| Thromboembolic disease \| 1

Disease ID	21
Disease	alpha-1-antitrypsin deficiency
Manually Symptom	UMLS \| Name(Total Manually Symptoms:21) C2186532 \| liver disease C1623038 \| cirrhosis C1555769 \| pulmonary disease C1512411 \| hepatocellular carcinoma C0340648 \| coronary artery dissection C0265797 \| congenital emphysema C0264393 \| panacinar emphysema C0042880 \| vitamin k deficiency C0035204 \| respiratory diseases C0034067 \| emphysema C0031036 \| polyarteritis nodosa C0030326 \| panniculitis C0027613 \| neonatal hepatitis C0024117 \| chronic obstructive lung disease C0024115 \| lung disease C0023890 \| liver cirrhosis C0023890 \| cirrhosis of the liver C0022354 \| cholestatic jaundice C0018995 \| haemochromatosis C0010520 \| cyanosis C0009763 \| conjunctivitis
Text Mined Symptom	UMLS \| Name \| Sentences' Count(Total Symptoms:7) C0013990 \| emphysema \| 12 C0023895 \| liver disease \| 4 C0030326 \| panniculitis \| 3 C0024115 \| lung disease \| 3 C0024115 \| pulmonary disease \| 2 C0004096 \| bronchial asthma \| 1 C0023890 \| cirrhosis \| 1

Manually Genotype(Total Text Mining Genotypes:0)
(Waiting for update.)

Text Mining Genotype(Total Genotypes:0)
(Waiting for update.)

All Snps(Total Genotypes:12)
snpId	pubmedId	geneId	geneSymbol	diseaseId	sourceId	sentence	score	Year	geneSymbol_dbSNP	CHROMOSOME	POS	REF	ALT
rs121912714	NA	5265	SERPINA1	umls:C0221757	CLINVAR	NA	0.438751952	NA	SERPINA1	14	94380949	T	A
rs17580	NA	5265	SERPINA1	umls:C0221757	CLINVAR	NA	0.438751952	NA	SERPINA1	14	94380925	T	A
rs199422210	NA	5265	SERPINA1	umls:C0221757	CLINVAR	NA	0.438751952	NA	SERPINA1	14	94382686	G	T,C,A
rs199422211	NA	5265	SERPINA1	umls:C0221757	CLINVAR	NA	0.438751952	NA	SERPINA1	14	94381067	T	A
rs267606950	NA	5265	SERPINA1	umls:C0221757	CLINVAR	NA	0.438751952	NA	SERPINA1	14	94382686	G	-
rs28929474	NA	5265	SERPINA1	umls:C0221757	CLINVAR	NA	0.438751952	NA	SERPINA1	14	94378610	C	T
rs28931570	NA	5265	SERPINA1	umls:C0221757	CLINVAR	NA	0.438751952	NA	SERPINA1	14	94383051	G	A
rs361525	26620975	7124	TNF	umls:C0221757	BeFree	Previous work has shown that COPD/chronic bronchitis subjects with alpha-1 antitrypsin deficiency with the rs361525 TNF-α single nucleotide polymorphism have 100 times more TNF-in spontaneous sputum than disease matched controls.	0.008001298	2015	TNF	6	31575324	G	A
rs55819880	NA	5265	SERPINA1	umls:C0221757	CLINVAR	NA	0.438751952	NA	SERPINA1	14	94383008	G	A
rs751235320	NA	5265	SERPINA1	umls:C0221757	CLINVAR	NA	0.438751952	NA	SERPINA1	14	94382591	C	A
rs764220898	NA	5265	SERPINA1	umls:C0221757	CLINVAR	NA	0.438751952	NA	SERPINA1	14	94381043	C	G
rs764325655	NA	5265	SERPINA1	umls:C0221757	CLINVAR	NA	0.438751952	NA	SERPINA1	14	94378547	-	G

GWASdb Annotation(Total Genotypes:0)
(Waiting for update.)

GWASdb Snp Trait(Total Genotypes:0)
(Waiting for update.)

Mapped by lexical matching(Total Items:1)
HP ID	HP Name	MP ID	MP Name	Annotation
HP:0001399	Hepatic failure	MP:0006138	congestive heart failure	cardiac output is insufficient to supply blood throughout the body, resulting in the accumulation of fluid in the lungs and other body tissues; it is related mainly to salt and water retention in the tissues rather than directly to reduced blood flow; blo

Mapped by homologous gene(Total Items:6)
HP ID	HP Name	MP ID	MP Name	Annotation
HP:0002097	Emphysema	MP:0020321	increased vascular endothelial cell apoptosis	increase in the timing or the number of vascular endothelial cells undergoing programmed cell death
HP:0000100	Nephrotic syndrome	MP:0020216	decreased circulating complement protein level	less than normal levels of the serum proteins that act sequentially to allow for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes
HP:0001399	Hepatic failure	MP:0020137	decreased bone mineralization	decrease in the rate at which minerals are deposited into bone
HP:0012115	Hepatitis	MP:0013716	hypolactation	partial failure, or reduced ability to produce or secrete milk from the mammary gland
HP:0002240	Hepatomegaly	MP:0020329	decreased capillary density	reduction in the number of capillaries in a given cross-sectional area of a tissue
HP:0000952	Jaundice	MP:0020215	impaired blood coagulation	impaired ability of the blood to clot

Disease ID	21
Disease	alpha-1-antitrypsin deficiency
Case	(Waiting for update.)

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