rs1800574 Rat Genome Database

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Variant: rs1800574 -  Homo sapiens

RGD ID: 8659722
RS ID: rs1800574
ClinVar ID: CV134679
Genic Status: GENIC
Type: SNV (SO:0001483) 
Associated Genes: HNF1A  
Reference Nucleotide: C
Variant Nucleotide: T
Position
Assembly Chr Position
GRCh37 12 121,416,864
GRCh38 12 120,979,061
JBrowse: View Region in Genome Browser (JBrowse)
Model



ClinVar Data
HGVS Name(s) Last Evaluated Molecular Consequence Clinical Significance Trait Synonyms
LRG_522t1:c.293C>T
LRG_522:g.5316C>T
NG_011731.2:g.5316C>T
NC_000012.12:g.120979061C>T
More... 		11/21/2020 missense|missense variant benign|likely benign AllHighlyPenetrant; Diabetes mellitus MODY type 3; Mason type diabetes; MODY type 3; MODY hepatocyte nuclear factor-1-alpha related; MODY, type III; none provided
Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
GWAS Catalog Data
GWAS Catalog Study Disease Trait Study Size Risk Allele Risk Allele Frequency P Value P Value MLOG SNP Passing QC Reported Odds Ratio or Beta-coefficient Ontology Accession PubMed
GCST009379 Type 2 diabetes 74,124 European ancestry cases, 824,006 European ancestry controls T 0.0296 2E-12 11.698970004336019 Affymetrix, Illumina [~ 27000000] (imputed) 1.14 PMID:30297969
GCST008972 Urate levels 288,649 European ancestry individuals, 125,725 East Asian ancestry individuals, 33,671 African American individuals, 9,037 South Asian ancestry individuals, 608 Hispanic individuals T 0.033 3E-14 13.522878745280337 Affymetrix, Illumina [8249849] (imputed) 0.0846 urate measurement (EFO:0004531)
 PMID:31578528
GCST007517 Type 2 diabetes up to 48,286 European ancestry cases, up to 250,671 European ancestry controls T 0.033 4E-7 6.3979400086720375 Affymetrix, Illumina [247470] 1.11 PMID:29632382
GCST007516 Type 2 diabetes (adjusted for BMI) 48,286 European ancestry cases, 250,671 European ancestry controls, 33,126 African American, East Asian, Hispanic/Latino or South Asian cases, 120,161 African American, East Asian, Hispanic/Latino or South Asian controls T NR 1E-7 7.0 Affymetrix, Illumina [247470] 1.1 PMID:29632382
GCST007518 Type 2 diabetes (adjusted for BMI) up to 48,286 European ancestry cases, up to 250,671 European ancestry controls T 0.033 2E-7 6.698970004336019 Affymetrix, Illumina [247470] 1.1 PMID:29632382
GCST008971 Urate levels 288,649 European ancestry individuals T 0.0314 3E-12 11.522878745280337 Affymetrix, Illumina [8217339] (imputed) 0.080982 urate measurement (EFO:0004531)
 PMID:31578528
GCST007515 Type 2 diabetes 48,286 European ancestry cases, 250,671 European ancestry controls, 33,126 African American, East Asian, Hispanic/Latino or South Asian cases, 120,161 African American, East Asian, Hispanic/Latino or South Asian controls T 0.029 6E-8 7.221848749616356 Affymetrix, Illumina [247470] 1.11 PMID:29632382
GCST90019516 Serum phosphate levels 312,888 European ancestry individuals, 5,568 African ancestry individuals, 6,685 South Asian ancestry individuals T NR 1E-13 13.0 Affymetrix [9000000] (imputed) 0.0543 blood phosphate measurement (EFO:0010972)
 PMID:33462484
GCST90019511 Insulin-like growth factor 1 levels 340,567 European ancestry individuals, 5,974 African ancestry individuals, 7,283 South Asian ancestry individuals T NR 5E-94 93.30102999566398 Affymetrix [9000000] (imputed) 0.1445 IGF-1 measurement (EFO:0004627)
 PMID:33462484
GCST90019518 Sex hormone-binding globulin levels 310,323 European ancestry individuals, 5,523 African ancestry individuals, 6,638 South Asian ancestry individuals T NR 2E-15 14.698970004336019 Affymetrix [9000000] (imputed) 0.0585 sex hormone-binding globulin measurement (EFO:0004696)
 PMID:33462484
GCST90019506 Estimated glomerular filtration rate 342,376 European ancestry individuals, 6,016 African ancestry individuals, 7,339 South Asian ancestry individuals T NR 9E-16 15.045757490560675 Affymetrix [9000000] (imputed) 0.0563 glomerular filtration rate (EFO:0005208)
 PMID:33462484
GCST90019502 Creatinine levels 342,376 European ancestry individuals, 6,016 African ancestry individuals, 7,339 South Asian ancestry individuals T NR 1E-15 15.0 Affymetrix [9000000] (imputed) 0.056 creatinine measurement (EFO:0004518)
 PMID:33462484
GCST90019507 Gamma glutamyl transferase levels 342,339 European ancestry individuals, 6,015 African ancestry individuals, 7,336 South Asian ancestry individuals T NR 2E-10 9.698970004336019 Affymetrix [9000000] (imputed) 0.0444 serum gamma-glutamyl transferase measurement (EFO:0004532)
 PMID:33462484
GCST90100220 Estimated glomerular filtration rate (creatinine) 1,205,871 European ancestry individuals, 168,300 East Asian ancestry individuals, 63,553 African ancestry individuals, 23,509 Hispanic or Latin American individuals, 22,103 African American individuals, 21,791 Central Asian or South Asian ancestry individuals, 1,502 Middle Eastern ancestry individuals, 939 other admixed ancestry individuals, 602 Native American ancestry individuals, 150 Asian ancestry individuals, 339 individuals T 0.0307 2E-22 21.69897000433602 Affymetrix, Illumina [12653804] (imputed) 9.72 glomerular filtration rate (EFO:0005208)
 PMID:35710981
GCST90103633 Estimated glomerular filtration rate (creatinine) 1,004,040 European ancestry individuals, 165,726 East Asian ancestry individuals, 13,842 African American individuals, 13,359 South Asian ancestry individuals, 4,961 Hispanic individuals, 2 individuals T 0.0289478937605887 2E-21 20.69897000433602 NR [13633840] (imputed) 0.0068 glomerular filtration rate (EFO:0005208)
 PMID:34272381
GCST90019524 Urate levels 342,087 European ancestry individuals, 6,011 African ancestry individuals, 7,328 South Asian ancestry individuals T NR 1E-14 14.0 Affymetrix [9000000] (imputed) 0.054 urate measurement (EFO:0004531)
 PMID:33462484
GCST90132183 Type 2 diabetes 251,740 European ancestry individuals, 139,705 East Asian ancestry individuals, 40,737 South Asian ancestry individuals, 27,417 Hispanic individuals, 30,167 African American individuals, 2,426 Zulu ancestry individuals T NR 8E-21 20.096910013008056 Affymetrix, Illumina [10454876] (imputed) 1.16 PMID:35551307
GCST90103634 Estimated glomerular filtration rate (creatinine) 1,004,040 European ancestry individuals T 0.03 5E-15 14.301029995663981 NR [13635145] (imputed) 0.0063 glomerular filtration rate (EFO:0005208)
 PMID:34272381
GCST90018979 Serum creatinine levels 344,104 European ancestry individuals, 150,266 East Asian ancestry individuals T NR 4E-14 13.397940008672037 Affymetrix, Illumina [20538295] (imputed) 0.0429 creatinine measurement (EFO:0004518)
 PMID:34594039
GCST90132184 Type 2 diabetes 251,740 European ancestry individuals T 0.029 3E-23 22.522878745280337 Affymetrix, Illumina [10454876] (imputed) 0.185 PMID:35551307

Variant Details
Variant Transcripts
Gene Symbol:HNF1A
Accession:NM_001306179
Location:EXON
Amino Acid Prediction: A to V (nonsynonymous)
Amino Acid Position: 98
Amino Acid Sequence
(Calculated using NCBI transcript definition)
MVSKLSQLQTELLAALLESGLSKEALIQALGEPGPYLLAGEGPLDKGESCGGGRGELAELPNGLGETRGSEDETDDDGED
FTPPILKELENLSPEEAVHQKAVVETLLQEDPWRVAKMVKSYLQQHNIPQREVVDTTGLNQSHLSQHLNKGTPMKTQKRA
ALYTWYVRKQREVAQQFTHAGQGGLIEEPTGDELPTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAE
CIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAFRHKLAMDTYSGPPPGPGPGPALPAHSSPGLPPPALSPSKVHGV
RYGQPATSETAEVPSSSGGPLVTVSTPLHQVSPTGLEPSHSLLSTEAKLVSAAGGPLPPVSTLTALHSLEQTSPGLNQQP
QNLIMASLPGVMTIGPGEPASLGPTFTNTGASTLVIGLASTQAQSVPVINSMGSSLTTLQPVQFSQPLHPSYQQPLMPPV
QSHVTQSPFMATMAQLQSPHALYSHKPEVAQYTHTGLLPQTMLITDTTNLSALASLTPTKQEAALLPQVFTSDTEASSES
GLHTPASQATTLHVPSQDPASIQHLQPAHRLSASPTVSSSSLVLYQSSDSSNGQSHLLPSNHSVIETFISTQMASSSQ*

Gene Symbol:HNF1A
Accession:XM_024449168
Location:EXON
Amino Acid Prediction: A to V (nonsynonymous)
Amino Acid Position: 98
Amino Acid Sequence
(Calculated using NCBI transcript definition)
MVSKLSQLQTELLAALLESGLSKEALIQALGEPGPYLLAGEGPLDKGESCGGGRGELAELPNGLGETRGSEDETDDDGED
FTPPILKELENLSPEEAVHQKAVVETLLQEDPWRVAKMVKSYLQQHNIPQREVVDTTGLNQSHLSQHLNKGTPMKTQKRA
ALYTWYVRKQREVAQQFTHAGQGGLIEEPTGDELPTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAE
CIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAFRHKLAMDTYSGPPPGPGPGPALPAHSSPGLPPPALSPSKVHGV
RYGQPATSETAEVPSSSGGPLVTVSTPLHQVSPTGLEPSHSLLSTEAKLVSAAGGPLPPVSTLTALHSLEQTSPGLNQQP
QNLIMASLPGVMTIGPGEPASLGPTFTNTGASTLVIGLASTQAQSVPVINSMGSSLTTLQPVQFSQPLHPSYQQPLMPPV
QSHVTQSPFMATMAQLQSPHALYSHKPEVAQYTHTGLLPQTMLITDTTNLSALASLTPTKQVRSRPAGPPLACDRAPHPH
IPRAQEAALLPQVFTSDTEASSESGLHTPASQATTLHVPSQDPASIQHLQPAHRLSASPTVSSSSLVLYQSSDSSNGQSH
LLPSNHSVIETFISTQMASSSQ*

Gene Symbol:HNF1A
Accession:NM_001406915
Location:EXON
Amino Acid Prediction: A to V (nonsynonymous)
Amino Acid Position: 98
Amino Acid Sequence
(Calculated using NCBI transcript definition)
MVSKLSQLQTELLAALLESGLSKEALIQALGEPGPYLLAGEGPLDKGESCGGGRGELAELPNGLGETRGSEDETDDDGED
FTPPILKELENLSPEEAVHQKAVVETLLQEDPWRVAKMVKSYLQQHNIPQREVVDTTGLNQSHLSQHLNKGTPMKTQKRA
ALYTWYVRKQREVAQQFTHAGQGGLIEEPTGDELPTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAE
CIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAFRHKLAMDTYSGPPPGPGPGPALPAHSSPGLPPPALSPSKVHGV
RYGQPATSETAEVPSSSGGPLVTVSTPLHQVSPTGLEPSHSLLSTEAKLVSAAGGPLPPVSTLTALHSLEQTSPGLNQQP
QNLIMASLPGVMTIGPGEPASLGPTFTNTGASTLVIALYSHKPEVAQYTHTGLLPQTMLITDTTNLSALASLTPTKQVFT
SDTEASSESGLHTPASQATTLHVPSQDPASIQHLQPAHRLSASPTVSSSSLVLYQSSDSSNGQSHLLPSNHSVIETFIST
QMASSSQ*

Gene Symbol:HNF1A
Accession:NM_000545
Location:EXON
Amino Acid Prediction: A to V (nonsynonymous)
Amino Acid Position: 98
Amino Acid Sequence
(Calculated using NCBI transcript definition)
MVSKLSQLQTELLAALLESGLSKEALIQALGEPGPYLLAGEGPLDKGESCGGGRGELAELPNGLGETRGSEDETDDDGED
FTPPILKELENLSPEEAVHQKAVVETLLQEDPWRVAKMVKSYLQQHNIPQREVVDTTGLNQSHLSQHLNKGTPMKTQKRA
ALYTWYVRKQREVAQQFTHAGQGGLIEEPTGDELPTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAE
CIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAFRHKLAMDTYSGPPPGPGPGPALPAHSSPGLPPPALSPSKVHGV
RYGQPATSETAEVPSSSGGPLVTVSTPLHQVSPTGLEPSHSLLSTEAKLVSAAGGPLPPVSTLTALHSLEQTSPGLNQQP
QNLIMASLPGVMTIGPGEPASLGPTFTNTGASTLVIGLASTQAQSVPVINSMGSSLTTLQPVQFSQPLHPSYQQPLMPPV
QSHVTQSPFMATMAQLQSPHALYSHKPEVAQYTHTGLLPQTMLITDTTNLSALASLTPTKQVFTSDTEASSESGLHTPAS
QATTLHVPSQDPASIQHLQPAHRLSASPTVSSSSLVLYQSSDSSNGQSHLLPSNHSVIETFISTQMASSSQ*
Variant Samples
Additional References at PubMed
PMID:8945470   PMID:9112026   PMID:9133564   PMID:9287053   PMID:10333057   PMID:10634407   PMID:11289470   PMID:12359128   PMID:12574234   PMID:12618559   PMID:12675668   PMID:15277395  
PMID:15761192   PMID:15928245   PMID:16046319   PMID:16186275   PMID:16917892   PMID:16963153   PMID:17033837   PMID:17116178   PMID:17192490   PMID:17425917   PMID:17440016   PMID:17496355  
PMID:17573900   PMID:17601994   PMID:17700391   PMID:17924661   PMID:17937063   PMID:18332101   PMID:18414213   PMID:18513305   PMID:24728327   PMID:25575005   PMID:25741868   PMID:26467025  
PMID:28492532   PMID:29895593   PMID:31109344   PMID:35328643  


Additional Information

Database Acc Id Source(s)
ClinVar RCV000117230 CLINVAR
  RCV000391875 CLINVAR
  RCV000445439 CLINVAR
  RCV000713791 CLINVAR
  RCV002226424 CLINVAR
  RCV003153378 CLINVAR
  RCV003315672 CLINVAR
dbSNP (RS) rs1800574 CLINVAR
GWAS Catalog GCST007515 GWAS Catalog
  GCST007516 GWAS Catalog
  GCST007517 GWAS Catalog
  GCST007518 GWAS Catalog
  GCST008971 GWAS Catalog
  GCST008972 GWAS Catalog
  GCST009379 GWAS Catalog
MedGen C0342276 CLINVAR
  C1140680 CLINVAR
  C1838100 CLINVAR
  C3661900 CLINVAR
  C3888631 CLINVAR
  CN074294 CLINVAR
  CN169374 CLINVAR
NCBI Gene HNF1A CLINVAR
OMIM 142410 CLINVAR
  144700 CLINVAR
  600496 CLINVAR
  606391 CLINVAR
SNOMED CT 28453007 CLINVAR