Database of Pathogenic Variants

Variant Detail

Variant Information

ID: DPV: 883
Chromosome: 11
Gene
HGVS (GRCh37/hg19): NC_000011.9:g.64361219G>A
HGVS (GRCh38/hg38): NC_000011.10:g.64593747G>A
HGVS (RNA): NM_144585.3:c.774G>A
HGVS (Protein): NP_653186.2:p.W258*
dbSNP: -
ClinGen Allele Registry: CA116312
Allele Frequency

Individual Information

ID

DPVS:636.1

Clinical Significance

Likely pathogenic

Date Last Evaluated

2017-03-30

Clinical Significance Citation

Enomoto, A. Molecular identification of a renal urate anion exchanger that regulates blood urate levels. 2002 Nature. 2002 May 23;417(6887):447-52. doi: 10.1038/nature742. Epub 2002 Apr 14. PMID:12024214

Tanaka, M. Two male siblings with hereditary renal hypouricemia and exercise-induced ARF. 2003 Am J Kidney Dis. 2003 Dec;42(6):1287-92. PMID:14655203

Komoda, F. The W258X mutation in SLC22A12 is the predominant cause of Japanese renal hypouricemia. 2004 Pediatr Nephrol. 2004 Jul;19(7):728-33. doi: 10.1007/s00467-004-1424-1. Epub 2004 Mar 31. PMID:15054642

Cheong, H. I. Mutational analysis of idiopathic renal hypouricemia in Korea. 2005 Pediatr Nephrol. 2005 Jul;20(7):886-90. doi: 10.1007/s00467-005-1863-3. Epub 2005 May 24. PMID:15912381

Komatsuda, A. Analysis of mutations in the urate transporter 1 (URAT1) gene of Japanese patients with hypouricemia in northern Japan and review of the literature. 2006 Ren Fail. 2006;28(3):223-7. PMID:16703794

Ichida, K. Age and origin of the G774A mutation in SLC22A12 causing renal hypouricemia in Japanese. 2008 Clin Genet. 2008 Sep;74(3):243-51. doi: 10.1111/j.1399-0004.2008.01021.x. Epub 2008 May 15. PMID:18492088

Lee, J. H. Prevalence of hypouricaemia and SLC22A12 mutations in healthy Korean subjects. 2008 Nephrology (Carlton). 2008 Dec;13(8):661-6. doi: 10.1111/j.1440-1797.2008.01029.x. Epub 2008 Nov 17. PMID:19019168

Hamajima, N. Serum uric acid distribution according to SLC22A12 W258X genotype in a cross-sectional study of a general Japanese population. 2011 BMC Med Genet. 2011 Mar 2;12:33. doi: 10.1186/1471-2350-12-33. PMID:21366895

Transcript

Disease

Hypouricemia renal 1
OMIM:220150
MedGen:C0473219

Phenotype

Zygosity

compound heterozygote

Allele Origin

germline

Affected Status

yes

Sample Type

Analysis Type

SEQuencing

Collection Method

clinical testing

Compound heterozygous variant(s)

Data Submitter

Comment

ID

DPVS:1424.1

Clinical Significance

Pathogenic

Date Last Evaluated

2018-01-30

Clinical Significance Citation

Fujita, K. A novel compound heterozygous mutation in the SLC22A12 (URAT1) gene in a Japanese patient associated with renal hypouricemia. 2016 Clin Chim Acta. 2016 Dec 1;463:119-121. doi: 10.1016/j.cca.2016.10.025. Epub 2016 Oct 22. PMID:27780716

Transcript

Disease

Phenotype

Zygosity

compound heterozygote

Allele Origin

germline

Affected Status

yes

Sample Type

Analysis Type

SEQuencing

Collection Method

literature only

Compound heterozygous variant(s)

Data Submitter

Comment

ID

DPVS:12201.1

Clinical Significance

Pathogenic

Date Last Evaluated

2020-01-08

Clinical Significance Citation

Wakida, N. Mutations in human urate transporter 1 gene in presecretory reabsorption defect type of familial renal hypouricemia. 2005 J Clin Endocrinol Metab. 2005 Apr;90(4):2169-74. doi: 10.1210/jc.2004-1111. Epub 2005 Jan 5. PMID:15634722

Fujinaga, S. Posterior reversible encephalopathy syndrome with exercise-induced acute kidney injury in renal hypouricemia type 1. 2013 Eur J Pediatr. 2013 Nov;172(11):1557-60. doi: 10.1007/s00431-013-1986-7. Epub 2013 Mar 23. PMID:23525542

Tanaka, M. Two male siblings with hereditary renal hypouricemia and exercise-induced ARF. 2003 Am J Kidney Dis. 2003 Dec;42(6):1287-92. doi: 10.1053/j.ajkd.2003.08.032. PMID:14655203

Transcript

Disease

Hypouricemia renal 1
OMIM:220150
MedGen:C0473219

Phenotype

Zygosity

homozygote

Allele Origin

germline

Affected Status

yes

Sample Type

Analysis Type

SEQuencing

Collection Method

literature only

Compound heterozygous variant(s)

Data Submitter

Comment

ID

DPVS:12202.1

Clinical Significance

Pathogenic

Date Last Evaluated

2020-01-08

Clinical Significance Citation

Tanaka, M. Two male siblings with hereditary renal hypouricemia and exercise-induced ARF. 2003 Am J Kidney Dis. 2003 Dec;42(6):1287-92. doi: 10.1053/j.ajkd.2003.08.032. PMID:14655203

Transcript

Disease

Hypouricemia renal 1
OMIM:220150
MedGen:C0473219

Phenotype

Zygosity

compound heterozygote

Allele Origin

germline

Affected Status

yes

Sample Type

Analysis Type

SEQuencing

Collection Method

literature only

Compound heterozygous variant(s)

Data Submitter

Comment

c.[774G>A];[1145A>T], [c.774G>A];[1639_1643delGTCCT], c.[774G>A];[1253T>G]

ID

DPVS:13175.2

Clinical Significance

Pathogenic

Date Last Evaluated

2020-07-03

Clinical Significance Citation

Ichida, K. Clinical and molecular analysis of patients with renal hypouricemia in Japan-influence of URAT1 gene on urinary urate excretion. 2004 J Am Soc Nephrol. 2004 Jan;15(1):164-73. doi: 10.1097/01.asn.0000105320.04395.d0. PMID:14694169

Transcript

Disease

Hypouricemia renal 1
OMIM:220150
MedGen:C0473219

Phenotype

Zygosity

compound heterozygote

Allele Origin

germline

Affected Status

yes

Sample Type

Analysis Type

Next-Generation Sequencing

Collection Method

clinical testing

Compound heterozygous variant(s)

Data Submitter

Comment

c.506+1G>A(;)774G>A|This variant was detected in  IRUD (Initiative on Rare and Undiagnosed Diseases) project.

ClinVar

Model Animals

VCF

VCF (GRCh37/hg19)

											##fileformat=VCFv4.0
##reference=GRCh37
##INFO=<ID=CLNALLELEID,Number=1,Type=Integer,Description="the ClinVar Allele ID">
##INFO=<ID=CLNDISDB,Number=.,Type=String,Description="Tag-value pairs of disease database name and identifier, e.g. OMIM:NNNNNN (from ClinVar)">
##INFO=<ID=CLNDN,Number=.,Type=String,Description="ClinVar's preferred disease name for the concept specified by disease identifiers in CLNDISDB (from ClinVar)">
##INFO=<ID=CLNHGVS,Number=.,Type=String,Description="Top-level (primary assembly, alt, or patch) HGVS expression.(from ClinVar)">
##INFO=<ID=CLNSIG,Number=.,Type=String,Description="Clinical significance for this single variant (from ClinVar)">
##INFO=<ID=EXAC_AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed (from ExAC r1)">
##INFO=<ID=EXAC_AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed (from ExAC r1)">
##INFO=<ID=EXAC_AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes (from ExAC r1)">
##INFO=<ID=EXAC_FILTER,Number=1,Type=String,Description="calculated by self of overlapping values in field FILTER (from ExAC r1)">
##INFO=<ID=GNOMAD_AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed (from gnomAD v2.1.1 )">
##INFO=<ID=GNOMAD_AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed (from gnomAD v2.1.1 )">
##INFO=<ID=GNOMAD_AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes (from gnomAD v2.1.1 )">
##INFO=<ID=HGVD_AAF,Number=A,Type=Float,Description="Alternative Allele Frequency(s) NA/(NR+NAtotal) (from HGVD/DBexome20170802)">
##INFO=<ID=HGVD_AC,Number=A,Type=Integer,Description="number(s) of alternative allele(s) (from HGVD/DBexome20170802)">
##INFO=<ID=HGVD_NR,Number=1,Type=Integer,Description="number of reference allele (from HGVD/DBexome20170802)">
##INFO=<ID=TOMMO_4_7K_AC,Number=A,Type=Integer,Description="Allele count in genotypes (from ToMMo 4.7KJPN (20190826))">
##INFO=<ID=TOMMO_4_7K_AF,Number=A,Type=Float,Description="Allele frequency, for each ALT allele, in the same order as listed  (from ToMMo 4.7KJPN (20190826))">
##INFO=<ID=TOMMO_4_7K_AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes (from ToMMo 4.7KJPN (20190826))">
##INFO=<ID=dbSNP_RSID,Number=1,Type=String,Description="dbSNP ID (from dbSNP b151 )">
##INFO=<ID=GENEINFO,Number=1,Type=String,Description="Pairs each of gene symbol:gene id. The gene symbol and id are delimited by a colon (:)">
##INFO=<ID=DPVID,Number=.,Type=String,Description="DPV Variant ID">
##INFO=<ID=DPVSIG,Number=.,Type=String,Description="Variant Clinical Significance">
##INFO=<ID=DPVDSDBID,Number=.,Type=String,Description="Variant disease database ID">
##INFO=<ID=DPVDBN,Number=.,Type=String,Description="Variant disease name">
##INFO=<ID=DPVHGVS,Number=.,Type=String,Description="Variant in HGVS.">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
11	64361219	NC_000011.9:g.64361219G>A	G	A	.	.	EXAC_AF=0.0002965;EXAC_AC=36;EXAC_AN=121410;GNOMAD_AF=0.00028341;GNOMAD_AC=71;GNOMAD_AN=250516;TOMMO_4_7K_AF=0.0231;TOMMO_4_7K_AC=220;TOMMO_4_7K_AN=9544;CLNALLELEID=18551;CLNDN=Familial_renal_hypouricemia;CLNDISDB=MONDO:MONDO:0020728,MedGen:C4551590,OMIM:220150,SNOMED_CT:236478009;CLNSIG=Pathogenic;CLNHGVS=NC_000011.9:g.64361219G>A;HGVD_AAF=0.0228;HGVD_NR=2359;HGVD_AC=55;GENEINFO=17989:116085;DPVID=883;DPVSIG=Likely_pathogenic|Pathogenic;DPVDSDBID=OMIM:220150|OMIM:612076;DPVDBN=Hypouricemia_renal_1|Hypouricemia_renal_2;DPVHGVS=NC_000011.9:g.64361219G>A	.

VCF (GRCh38/hg38)

											##fileformat=VCFv4.0
##reference=GRCh38
##INFO=<ID=CLNALLELEID,Number=1,Type=Integer,Description="the ClinVar Allele ID">
##INFO=<ID=CLNDISDB,Number=.,Type=String,Description="Tag-value pairs of disease database name and identifier, e.g. OMIM:NNNNNN (from ClinVar)">
##INFO=<ID=CLNDN,Number=.,Type=String,Description="ClinVar's preferred disease name for the concept specified by disease identifiers in CLNDISDB (from ClinVar)">
##INFO=<ID=CLNHGVS,Number=.,Type=String,Description="Top-level (primary assembly, alt, or patch) HGVS expression.(from ClinVar)">
##INFO=<ID=CLNSIG,Number=.,Type=String,Description="Clinical significance for this single variant (from ClinVar)">
##INFO=<ID=GNOMAD_AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed (from gnomAD v2.1.1 )">
##INFO=<ID=GNOMAD_AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed (from gnomAD v2.1.1 )">
##INFO=<ID=GNOMAD_AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes (from gnomAD v2.1.1 )">
##INFO=<ID=dbSNP_RSID,Number=1,Type=String,Description="dbSNP ID (from dbSNP b151 )">
##originalFile=</tmp/crossmap-input-6solf93g>
##targetRefGenome=</usr/lib64/python2.7/site-packages/transvar/transvar.download/hg38.fa>
##INFO=<ID=GENEINFO,Number=1,Type=String,Description="Pairs each of gene symbol:gene id. The gene symbol and id are delimited by a colon (:)">
##INFO=<ID=DPVID,Number=.,Type=String,Description="DPV Variant ID">
##INFO=<ID=DPVSIG,Number=.,Type=String,Description="Variant Clinical Significance">
##INFO=<ID=DPVDSDBID,Number=.,Type=String,Description="Variant disease database ID">
##INFO=<ID=DPVDBN,Number=.,Type=String,Description="Variant disease name">
##INFO=<ID=DPVHGVS,Number=.,Type=String,Description="Variant in HGVS.">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
11	64593747	NC_000011.9:g.64361219G>A	G	A	.	.	dbSNP_RSID=rs121907892;GNOMAD_AF=0.00028341;GNOMAD_AC=71;GNOMAD_AN=250516;CLNALLELEID=18551;CLNDN=Familial_renal_hypouricemia;CLNDISDB=MONDO:MONDO:0020728,MedGen:C0473219,OMIM:220150,SNOMED_CT:236478009;CLNSIG=Pathogenic;CLNHGVS=NC_000011.10:g.64593747G>A;GENEINFO=17989:116085;DPVID=883;DPVSIG=Likely_pathogenic|Pathogenic;DPVDSDBID=OMIM:220150|OMIM:612076;DPVDBN=Hypouricemia_renal_1|Hypouricemia_renal_2;DPVHGVS=NC_000011.10:g.64593747G>A	.