rs2228570 Rat Genome Database

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Variant: rs2228570 -  Homo sapiens

RGD ID: 11614866
RS ID: rs2228570
ClinVar ID: CV331088
Genic Status: GENIC
Type: SNV (SO:0001483) 
Associated Genes: VDR  
Reference Nucleotide: A
Variant Nucleotide: G
Position
Assembly Chr Position
GRCh37 12 48,272,895
GRCh38 12 47,879,112
JBrowse: View Region in Genome Browser (JBrowse)
Model



ClinVar Data
HGVS Name(s) Last Evaluated Molecular Consequence Clinical Significance Trait Synonyms
NG_008731.1:g.30920T>C
NC_000012.12:g.47879112A>G
NC_000012.11:g.48272895A>G
NP_001017535.1:p.Met1Thr
More... 		10/18/2022 initiatior codon variant|initiator_codon_variant|missense variant benign|conflicting interpretations of pathogenicity|drug response AllHighlyPenetrant; GENERALIZED RESISTANCE TO 1,25-DIHYDROXYVITAMIN D; HYPOCALCEMIC VITAMIN D-RESISTANT RICKETS; none provided; PDDR IIA; PSEUDOVITAMIN D-DEFICIENCY, TYPE IIA; RICKETS, HEREDITARY VITAMIN D-RESISTANT; RICKETS-ALOPECIA SYNDROME; VITAMIN D-DEPENDENT RICKETS, TYPE 2A; VITAMIN D-DEPENDENT RICKETS, TYPE 2A, WITH OR WITHOUT ALOPECIA; VITAMIN D-RESISTANT RICKETS WITH END-ORGAN UNRESPONSIVENESS TO 1,25-DIHYDROXYCHOLECALCIFEROL
Disease Annotations     Click to see Annotation Detail View

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
GCST90002382 Eosinophil percentage of white cells 408,112 British individuals G 0.614879 1E-9 9.0 Affymetrix [93095623] (imputed) 0.0138518615 eosinophil percentage of leukocytes (EFO:0007991)
 PMID:32888494
GCST007065 Eosinophil counts approximately 440,000 European ancestry individuals ? NR 6E-9 8.221848749616356 NR [~ 8900000] (imputed) N/A eosinophil count (EFO:0004842)
 PMID:30595370

Variant Details
Variant Transcripts
Gene Symbol:VDR
Accession:NM_001017535
Location:EXON

Gene Symbol:VDR
Accession:NM_001364085
Location:EXON

Gene Symbol:VDR
Accession:NM_001374662
Location:EXON

Gene Symbol:VDR
Accession:XM_047429500
Location:EXON

Gene Symbol:VDR
Accession:XM_024449178
Location:EXON
Amino Acid Prediction: M to T (nonsynonymous)
Amino Acid Position: 24
Amino Acid Sequence
(Calculated using NCBI transcript definition)
MEWRNKKRSDWLSMVLRTAGVEGTEAMAASTSLPDPGDFDRNVPRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKAL
FTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTDEEVQRKREMILKRKEEEALKDSLRPKLSEEQQRIIAILLD
AHHKTYDPTYSDFCQFRPPVRVNDGGGSHPSRPNSRHTPSFSGDSSSSCSDHCITSSDMMDSSSFSNLDLSEEDSDDPSV
TLELSQLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDMSWTCGNQDYKYRV
SDVTKAGHSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQDRLSNTLQTYIRCRHPPPGSH
LLYAKMIQKLADLRSLNEEHSKQYRCLSFQPECSMKLTPLVLEVFGNEIS*

Gene Symbol:VDR
Accession:NM_000376
Location:EXON

Gene Symbol:VDR
Accession:NM_001017536
Location:EXON
Amino Acid Prediction: M to T (nonsynonymous)
Amino Acid Position: 51
Amino Acid Sequence
(Calculated using NCBI transcript definition)
MEWRNKKRSDWLSMVLRTAGVEEAFGSEVSVRPHRRAPLGSTYLPPAPSGTEAMAASTSLPDPGDFDRNVPRICGVCGDR
ATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTDEEVQRKREMILKR
KEEEALKDSLRPKLSEEQQRIIAILLDAHHKTYDPTYSDFCQFRPPVRVNDGGGSHPSRPNSRHTPSFSGDSSSSCSDHC
ITSSDMMDSSSFSNLDLSEEDSDDPSVTLELSQLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEV
IMLRSNESFTMDDMSWTCGNQDYKYRVSDVTKAGHSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAA
LIEAIQDRLSNTLQTYIRCRHPPPGSHLLYAKMIQKLADLRSLNEEHSKQYRCLSFQPECSMKLTPLVLEVFGNEIS*

Gene Symbol:VDR
Accession:NM_001374661
Location:EXON

Variant Samples
Additional References at PubMed
PMID:24033266   PMID:25741868   PMID:28492532   PMID:35738466  


Additional Information

Database Acc Id Source(s)
ClinVar RCV000601968 CLINVAR
  RCV000988816 CLINVAR
  RCV001512350 CLINVAR
dbSNP (RS) rs2228570 CLINVAR
GWAS Catalog GCST90002382 GWAS Catalog
MedGen C0342646 CLINVAR
  C3661900 CLINVAR
  CN169374 CLINVAR
NCBI Gene VDR CLINVAR
OMIM 277440 CLINVAR
  601769 CLINVAR
SNOMED CT 237894002 CLINVAR