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	cystinuria

Disease ID	23
Disease	cystinuria
Definition	An inherited disorder due to defective reabsorption of CYSTINE and other BASIC AMINO ACIDS by the PROXIMAL RENAL TUBULES. This form of aminoaciduria is characterized by the abnormally high urinary levels of cystine; LYSINE; ARGININE; and ORNITHINE. Mutations involve the amino acid transport protein gene SLC3A1.
Synonym	csnu csnu - cystinuria csnu1, formerly csnu3, formerly cystinuria (disorder) cystinuria [disease/finding] cystinuria, nos cystinuria, type i, formerly cystinuria, type ii, formerly cystinuria, type iii, formerly cystinuria, type non-i, formerly cystinurias high urine cystine levels
Orphanet	ORPHANET:214
OMIM	OMIM:220100
DOID	DOID:9266
ICD10	ICD10CM:E72.01
UMLS	C0010691
MeSH	D003555
SNOMED-CT	SNOMEDCT_US_2016_09_01:85020001
Comorbidity	UMLS \| Disease \| Sentences' Count(Total Sentences:3) C0025362 \| mental retardation \| 1 C0270960 \| congenital myopathy \| 1 C0026848 \| myopathy \| 1
Curated Gene	Entrez_id \| Symbol \| Resource(Total Genes:2) 11136 \| SLC7A9 \| CLINVAR;GHR;ORPHANET;UniProtKB-KW;UNIPROT;CTD_human 6519 \| SLC3A1 \| CLINVAR;GHR;ORPHANET;UniProtKB-KW;UNIPROT;CTD_human
Inferring Gene	Entrez_id \| Symbol \| Resource(Total Genes:3) 6519 \| SLC3A1 \| CIPHER;CTD_human 30061 \| SLC40A1 \| CIPHER 11136 \| SLC7A9 \| CIPHER;CTD_human
Text Mined Gene	Entrez_id \| Symbol \| Score \| Resource(Total Genes:31) 10157 \| AASS \| 3.301 \| DISEASES 103 \| ADAR \| 1.082 \| DISEASES 55811 \| ADCY10 \| 4.458 \| DISEASES 229 \| ALDOB \| 1.143 \| DISEASES 353 \| APRT \| 2.558 \| DISEASES 79823 \| CAMKMT \| 4.55 \| DISEASES 846 \| CASR \| 1.659 \| DISEASES 1184 \| CLCN5 \| 2.653 \| DISEASES 1188 \| CLCNKB \| 1.387 \| DISEASES 1269 \| CNR2 \| 1.431 \| DISEASES 1491 \| CTH \| 2.701 \| DISEASES 8029 \| CUBN \| 1.274 \| DISEASES 2159 \| F10 \| 3.24 \| DISEASES 2710 \| GK \| 1.862 \| DISEASES 84557 \| MAP1LC3A \| 1.443 \| DISEASES 4952 \| OCRL \| 1.297 \| DISEASES 5091 \| PC \| 1.367 \| DISEASES 5550 \| PREP \| 1.647 \| DISEASES 5625 \| PRODH \| 1.393 \| DISEASES 53635 \| PTOV1 \| 2.054 \| DISEASES 1827 \| RCAN1 \| 1.297 \| DISEASES 6338 \| SCNN1B \| 1.804 \| DISEASES 6564 \| SLC15A1 \| 1.632 \| DISEASES 6510 \| SLC1A5 \| 1.356 \| DISEASES 6569 \| SLC34A1 \| 1.845 \| DISEASES 142680 \| SLC34A3 \| 1.736 \| DISEASES 6520 \| SLC3A2 \| 5.549 \| DISEASES 348932 \| SLC6A18 \| 5.371 \| DISEASES 84679 \| SLC9A7 \| 2.171 \| DISEASES 8802 \| SUCLG1 \| 1.961 \| DISEASES 7498 \| XDH \| 1.6 \| DISEASES
Locus	(Waiting for update.)

Disease ID	23
Disease	cystinuria
Integrated Phenotype	HPO \| Name(Total Integrated Phenotypes:5) HP:0000790 \| Hematuria HP:0004337 \| Abnormality of amino acid metabolism HP:0000787 \| Nephrolithiasis HP:0002149 \| Hyperuricemia HP:0000083 \| Renal insufficiency
Text Mined Phenotype	HPO \| Name \| Sentences' Count(Total Phenotypes:3) HP:0003198 \| Myopathic changes \| 1 HP:0001249 \| Mental retardation \| 1 HP:0011968 \| Feeding difficulties \| 1

Disease ID	23
Disease	cystinuria
Manually Symptom	UMLS \| Name(Total Manually Symptoms:16) C2720373 \| phenylketonuria C2700591 \| muckle-wells syndrome C2697388 \| cystathioninuria C1963165 \| malabsorption C0751378 \| neurologic signs C0740394 \| uricemia C0451641 \| urolithiasis C0451641 \| urinary lithiasis C0406549 \| acquired cutis laxa C0392525 \| nephrolithiasis C0265275 \| jeune syndrome C0238409 \| squamous cell carcinoma of the renal pelvis C0041952 \| ureterolithiasis C0035334 \| retinitis pigmentosa C0030486 \| paraplegia C0015411 \| eye manifestations
Text Mined Symptom	(Waiting for update.)

Manually Genotype(Total Manually Genotypes:2)
Gene	Mutation	DOI	Article Title
SLC3A1	p.M467T	doi:10.1038/gim.2015.123	Expanded genetic screening panel for the Ashkenazi Jewish population
SLC7A9	p.A182T	doi:10.1038/gim.2015.123	Expanded genetic screening panel for the Ashkenazi Jewish population

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

All Snps(Total Genotypes:25)
snpId	pubmedId	geneId	geneSymbol	diseaseId	sourceId	sentence	score	Year	geneSymbol_dbSNP	CHROMOSOME	POS	REF	ALT
rs121908479	11013083	11136	SLC7A9	umls:C0010691	BeFree	Applying two methods for linkage disequilibrium analysis to haplotype data spanning six 19q12-q13.1 polymorphic markers, and relying on the physical distances between the markers and the recently mapped SLC7A9 (CSNU3) locus, the age of the founder missense V170M mutation causing non-type I cystinuria in Jews of Libyan ancestry is calculated to be approximately 14 to 15 generations (g) (95% confidence interval: 9-20 g) or slightly more.	0.609135824	2000	SLC7A9	19	32862557	C	T
rs121908479	NA	11136	SLC7A9	umls:C0010691	CLINVAR	NA	0.609135824	NA	SLC7A9	19	32862557	C	T
rs121908480	19782624	11136	SLC7A9	umls:C0010691	UNIPROT	In conclusion, we developed a reliable and robust MLPA analytic method for SLC3A1 and SLC7A9 genes that represents an optimal complement to DNA sequence analysis in patients with cystinuria, enabling the screening for deletions and duplications.	0.609135824	2010	SLC7A9	19	32864261	C	T
rs121908480	NA	11136	SLC7A9	umls:C0010691	CLINVAR	NA	0.609135824	NA	SLC7A9	19	32864261	C	T
rs121908482	NA	11136	SLC7A9	umls:C0010691	CLINVAR	NA	0.609135824	NA	SLC7A9	19	32862482	C	T
rs121908483	NA	11136	SLC7A9	umls:C0010691	CLINVAR	NA	0.609135824	NA	SLC7A9	19	32859939	C	T
rs121908484	NA	11136	SLC7A9	umls:C0010691	CLINVAR	NA	0.609135824	NA	SLC7A9	19	32843932	G	A
rs121908485	NA	11136	SLC7A9	umls:C0010691	CLINVAR	NA	0.609135824	NA	SLC7A9	19	32864733	A	G
rs121908486	NA	11136	SLC7A9	umls:C0010691	CLINVAR	NA	0.609135824	NA	SLC7A9	19	32859932	G	A
rs121908487	NA	11136	SLC7A9	umls:C0010691	CLINVAR	NA	0.609135824	NA	SLC7A9	19	32862127	T	C
rs121912691	10798361	6519	SLC3A1	umls:C0010691	BeFree	Association between M467T and 114 C-->A variants within the SLC3A1 gene and some phenotypical traits in cystinuria patients from Spain.	0.608573077	2000	SLC3A1	2	44312653	T	A,C
rs121912691	NA	6519	SLC3A1	umls:C0010691	CLINVAR	NA	0.608573077	NA	SLC3A1	2	44312653	T	A,C
rs121912691	11432486	6519	SLC3A1	umls:C0010691	BeFree	M467T mutation (exon 8) in rBAT gene is found to be the most common mutation in cystinuria type I patients.	0.608573077	2001	SLC3A1	2	44312653	T	A,C
rs121912694	NA	6519	SLC3A1	umls:C0010691	CLINVAR	NA	0.608573077	NA	SLC3A1	2	44280827	G	A,T
rs121912697	NA	6519	SLC3A1	umls:C0010691	CLINVAR	NA	0.608573077	NA	SLC3A1	2	44301076	G	A
rs144162964	11748844	6519	SLC3A1	umls:C0010691	UNIPROT	Identification of 12 novel mutations in the SLC3A1 gene in Swedish cystinuria patients.	0.608573077	2001	SLC3A1	2	44312634	T	C
rs146815072	16609684	11136	SLC7A9	umls:C0010691	UNIPROT	A novel missense mutation of SLC7A9 frequent in Japanese cystinuria cases affecting the C-terminus of the transporter.	0.609135824	2006	SLC7A9	19	32830639	G	A
rs374267248	14561219	55238	SLC38A7	umls:C0010691	BeFree	Cystinuria-specific rBAT(R365W) mutation reveals two translocation pathways in the amino acid transporter rBAT-b0,+AT.	0.003800186	2004	SLC38A7	16	58671183	G	A
rs387907276	NA	6519	SLC3A1	umls:C0010691	CLINVAR	NA	0.608573077	NA	SLC3A1	2	44313931	T	A
rs531029519	15635077	11136	SLC7A9	umls:C0010691	UNIPROT	164 probands from the International Cystinuria Consortium were screened for mutations in SLC3A1 (type A) and SLC7A9 (type B) and classified on the basis of urine excretion of cystine and dibasic amino acids by obligate heterozygotes into 37 type I (silent heterozygotes), 46 type non-I (hyperexcretor heterozygotes), 14 mixed, and 67 untyped probands.	0.609135824	2005	SLC7A9	19	32862503	C	G,T
rs79389353	NA	11136	SLC7A9	umls:C0010691	CLINVAR	NA	0.609135824	NA	SLC7A9	19	32862521	C	A,T
rs79389353	19782624	11136	SLC7A9	umls:C0010691	UNIPROT	In conclusion, we developed a reliable and robust MLPA analytic method for SLC3A1 and SLC7A9 genes that represents an optimal complement to DNA sequence analysis in patients with cystinuria, enabling the screening for deletions and duplications.	0.609135824	2010	SLC7A9	19	32862521	C	A,T
rs797044609	NA	6519	SLC3A1	umls:C0010691	CLINVAR	NA	0.608573077	NA	SLC3A1	2	44304282	-	TG
rs79987078	19782624	11136	SLC7A9	umls:C0010691	UNIPROT	In conclusion, we developed a reliable and robust MLPA analytic method for SLC3A1 and SLC7A9 genes that represents an optimal complement to DNA sequence analysis in patients with cystinuria, enabling the screening for deletions and duplications.	0.609135824	2010	SLC7A9	19	32864206	G	A
rs79987078	NA	11136	SLC7A9	umls:C0010691	CLINVAR	NA	0.609135824	NA	SLC7A9	19	32864206	G	A

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:0000083	Renal insufficiency	MP:0003335	exocrine pancreatic insufficiency	inadequate synthesis and/or secretion of digestive enzymes by the exocrine portion of the pancreas, usually due to loss of acinar tissue from idiopathic atrophy or acute or chronic inflammation, causing maldigestion and malabsorption of nutrients

Mapped by homologous gene(Total Items:4)
HP ID	HP Name	MP ID	MP Name	Annotation
HP:0002149	Hyperuricemia	MP:0020316	decreased vascular endothelial cell proliferation	decrease in the expansion rate of any vascular endothelial cell population by cell division
HP:0000790	Hematuria	MP:0020316	decreased vascular endothelial cell proliferation	decrease in the expansion rate of any vascular endothelial cell population by cell division
HP:0000083	Renal insufficiency	MP:0020316	decreased vascular endothelial cell proliferation	decrease in the expansion rate of any vascular endothelial cell population by cell division
HP:0000787	Nephrolithiasis	MP:0020316	decreased vascular endothelial cell proliferation	decrease in the expansion rate of any vascular endothelial cell population by cell division

Disease ID	23
Disease	cystinuria
Case	(Waiting for update.)