rs11555039 Rat Genome Database

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Variant: rs11555039 -  Homo sapiens

RGD ID: 8659400
RS ID: rs11555039
ClinVar ID: CV134324
Genic Status: GENIC
Type: SNV (SO:0001483) 
Associated Genes: CTSD  
Reference Nucleotide: A
Variant Nucleotide: G
Position
Assembly Chr Position
GRCh37 11 1,780,205
GRCh38 11 1,758,975
JBrowse: View Region in Genome Browser (JBrowse)
Model



ClinVar Data
HGVS Name(s) Last Evaluated Molecular Consequence Clinical Significance Trait Synonyms
NG_008655.1:g.10018T>C
NC_000011.10:g.1758975A>G
NC_000011.9:g.1780205A>G
NP_001900.1:p.Thr155=
More... 		05/07/2018 synonymous variant benign|likely benign|conflicting interpretations of pathogenicity AllHighlyPenetrant; Ceroid lipofuscinosis neuronal Cathepsin D-deficient; Ceroid storage disease; CTSD-Related Neuronal Ceroid-Lipofuscinosis; Neuronal ceroid lipofuscinosis due to Cathepsin D deficiency; none provided
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
GCST90011899 Aspartate aminotransferase levels 389,565 European ancestry individuals G 0.086 9E-13 12.045757490560675 Affymetrix [4314223] (imputed) 7.14 aspartate aminotransferase measurement (EFO:0004736)
 PMID:33547301
GCST90018944 Aspartate aminotransferase levels 342,990 European ancestry individuals, 150,068 East Asian ancestry individuals G NR 6E-14 13.221848749616356 Affymetrix, Illumina [20538469] (imputed) 0.0296 aspartate aminotransferase measurement (EFO:0004736)
 PMID:34594039

Variant Details
Variant Transcripts
Gene Symbol:CTSD
Accession:NM_001909
Location:EXON
Amino Acid Prediction: T to T (synonymous)
Amino Acid Position: 155
Amino Acid Sequence
(Calculated using NCBI transcript definition)
MQPSSLLPLALCLLAAPASALVRIPLHKFTSIRRTMSEVGGSVEDLIAKGPVSKYSQAVPAVTEGPIPEVLKNYMDAQYY
GEIGIGTPPQCFTVVFDTGSSNLWVPSIHCKLLDIACWIHHKYNSDKSSTYVKNGTSFDIHYGSGSLSGYLSQDTVSVPC
QSASSASALGGVKVERQVFGEATKQPGITFIAAKFDGILGMAYPRISVNNVLPVFDNLMQQKLVDQNIFSFYLSRDPDAQ
PGGELMLGGTDSKYYKGSLSYLNVTRKAYWQVHLDQVEVASGLTLCKEGCEAIVDTGTSLMVGPVDEVRELQKAIGAVPL
IQGEYMIPCEKVSTLPAITLKLGGKGYKLSPEDYTLKVSQAGKTLCLSGFMGMDIPPPSGPLWILGDVFIGRYYTVFDRD
NNRVGFAEAARL*
Variant Samples
Additional References at PubMed
PMID:25741868   PMID:26467025   PMID:28492532  


Additional Information

Database Acc Id Source(s)
ClinVar RCV000116856 CLINVAR
  RCV000625344 CLINVAR
  RCV000675955 CLINVAR
  RCV001517364 CLINVAR
  RCV002312086 CLINVAR
dbSNP (RS) rs11555039 CLINVAR
GWAS Catalog GCST90011899 GWAS Catalog
MedGen C0027877 CLINVAR
  C0950123 CLINVAR
  C1864669 CLINVAR
  C3661900 CLINVAR
  CN169374 CLINVAR
NCBI Gene CTSD CLINVAR
OMIM 116840 CLINVAR
  610127 CLINVAR
SNOMED CT 42012007 CLINVAR