rs2904552 Rat Genome Database

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Variant: rs2904552 -  Homo sapiens

RGD ID: 8596252
RS ID: rs2904552
ClinVar ID: CV19050
Genic Status: GENIC
Type: SNV (SO:0001483) 
Associated Genes: PRODH  
Reference Nucleotide: C
Variant Nucleotide: T
Position
Assembly Chr Position
GRCh37 22 18,905,964
GRCh38 22 18,918,451
JBrowse: View Region in Genome Browser (JBrowse)
Model



ClinVar Data
HGVS Name(s) Last Evaluated Molecular Consequence Clinical Significance Age of Onset Trait Synonyms
NC_000022.11:g.18918451C>T
NC_000022.10:g.18905964C>T
NM_001195226.2:c.968G>A
NP_001182155.2:p.Arg323His
More... 		04/29/2022 missense|missense variant pathogenic|likely pathogenic|risk factor|benign|conflicting interpretations of pathogenicity|uncertain significance all ages|variable Hyperprolinemia type 1; PROLINE OXIDASE DEFICIENCY; SCHIZOPHRENIA SUSCEPTIBILITY LOCUS, CHROMOSOME 22q11-RELATED; SCHIZOPHRENIA, SUSCEPTIBILITY TO, 4
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
GCST90267284 Height (standard GWA) 283,749 European ancestry individuals T NR 5E-8 7.301029995663981 NR [7296935] (imputed) 0.16106 body height (EFO:0004339)
 PMID:37106081
GCST90265593 Plasma N-acetylproline levels in chronic kidney disease 4,936 European ancestry individuals T 0.11 3E-13 12.522878745280337 Illumina [7724667] (imputed) 0.161 metabolite measurement (EFO:0004725)
 PMID:37277652
GCST90265872 Plasma proline levels in chronic kidney disease 4,960 European ancestry individuals T 0.11 4E-66 65.39794000867204 Illumina [7723840] (imputed) 0.181 proline measurement (EFO:0009773)
 PMID:37277652
GCST90245723 X-23639 levels 14,296 European ancestry individuals T 0.1108 1E-12 12.0 Affymetrix [NR] (imputed) 0.11859422 X-23639 measurement (EFO:0800853)
 PMID:36357675
GCST006433 Heel bone mineral density 394,929 European ancestry individuals ? NR 8E-12 11.096910013008056 Affymetrix [20259828] (imputed) 0.0233085 heel bone mineral density (EFO:0009270)
 PMID:30048462
GCST007066 Heel bone mineral density approximately 446,000 European ancestry individuals ? NR 4E-9 8.397940008672037 NR [~ 8900000] (imputed) N/A heel bone mineral density (EFO:0009270)
 PMID:30595370
GCST90178477 Metabolite peak levels (QI9211) 2,466 Black/admixed ancestry individuals T NR 2E-12 11.698970004336019 Illumina [161106] 0.548055 metabolite measurement (EFO:0004725)
 PMID:35995766
GCST007841 Height approximately 458,000 European ancestry individuals ? NR 2E-8 7.698970004336019 NR [~ 8900000] (imputed) N/A body height (EFO:0004339)
 PMID:30595370
GCST90176332 Proline levels 2,466 Black/admixed ancestry individuals T NR 6E-16 15.221848749616356 Illumina [157711] 0.629148 proline measurement (EFO:0009773)
 PMID:35995766
GCST90178267 Metabolite peak levels (QI6976) 2,466 Black/admixed ancestry individuals T NR 9E-14 13.045757490560675 Illumina [158132] 0.578828 metabolite measurement (EFO:0004725)
 PMID:35995766
GCST90178269 Metabolite peak levels (QI6983) 2,466 Black/admixed ancestry individuals T NR 3E-12 11.522878745280337 Illumina [155367] 0.540754 metabolite measurement (EFO:0004725)
 PMID:35995766
GCST90178270 Metabolite peak levels (QI6984) 2,466 Black/admixed ancestry individuals T NR 3E-11 10.522878745280337 Illumina [157770] 0.516642 metabolite measurement (EFO:0004725)
 PMID:35995766
GCST90178271 Metabolite peak levels (QI6985) 2,466 Black/admixed ancestry individuals T NR 4E-11 10.397940008672037 Illumina [158015] 0.517029 metabolite measurement (EFO:0004725)
 PMID:35995766
GCST90178273 Metabolite peak levels (QI6991) 2,466 Black/admixed ancestry individuals T NR 8E-15 14.096910013008056 Illumina [161217] 0.60285 metabolite measurement (EFO:0004725)
 PMID:35995766

Variant Details
Variant Transcripts
Gene Symbol:PRODH
Accession:NM_001195226
Location:EXON
Amino Acid Prediction: R to H (nonsynonymous)
Amino Acid Position: 323
Amino Acid Sequence
(Calculated using NCBI transcript definition)
MKMTFYGHFVAGEDQESIQPLLRHYRAFGVSAILDYGVEEDLSPEEAEHKEMESCTSAAERDGSGTNKRDKQYQAHWAFG
DRRNGVISARTYFYANEAKCDSHMETFLRCIEASGRVSDDGFIAIKLTALGRPQFLLQFSEVLAKWRCFFHQMAVEQGQA
GLAAMDTKLEVAVLQESVAKLGIASRAEIEDWFTAETLGVSGTMDLLDWSSLIDSRTKLSKHLVVPNAQTGQLEPLLSRF
TEEEELQMTRMLQRMDVLAKKATEMGVRLMVDAEQTYFQPAISRLTLEMQRKFNVEKPLIFNTYQCYLKDAYDNVTLDVE
LAHREGWCFGAKLVRGAYLAQERARAAEIGYEDPINPTYEATNAMYHRCLDYVLEELKHNAKAKVMVASHNEDTVRFALR
RMEELGLHPADHRVYFGQLLGMCDQISFPLGQAGYPVYKYVPYGPVMEVLPYLSRRALENSSLMKGTHRERQLLWLELLR
RLRTGNLFHRPA*

Gene Symbol:LOC102724788
Accession:NM_001368250
Location:EXON
Amino Acid Prediction: R to H (nonsynonymous)
Amino Acid Position: 323
Amino Acid Sequence
(Calculated using NCBI transcript definition)
MKMTFYGHFVAGEDQESIQPLLRHYRAFGVSAILDYGVEEDLSPEEAEHKEMESCTSAAERDGSGTNKRDKQYQAHWAFG
DRRNGVISARTYFYANEAKCDSHMETFLRCIEASGRVSDDGFIAIKLTALGRPQFLLQFSEVLAKWRCFFHQMAVEQGQA
GLAAMDTKLEVAVLQESVAKLGIASRAEIEDWFTAETLGVSGTMDLLDWSSLIDSRTKLSKHLVVPNAQTGQLEPLLSRF
TEEEELQMTRMLQRMDVLAKKATEMGVRLMVDAEQTYFQPAISRLTLEMQRKFNVEKPLIFNTYQCYLKDAYDNVTLDVE
LAHREGWCFGAKLVRGAYLAQERARAAEIGYEDPINPTYEATNAMYHRCLDYVLEELKHNAKAKVMVASHNEDTVRFALR
RMEELGLHPADHRVYFGQLLGMCDQISFPLGQAGYPVYKYVPYGPVMEVLPYLSRRALENSSLMKGTHRERQLLWLELLR
RLRTGNLFHRPA*

Gene Symbol:PRODH
Accession:NM_016335
Location:EXON
Amino Acid Prediction: R to H (nonsynonymous)
Amino Acid Position: 431
Amino Acid Sequence
(Calculated using NCBI transcript definition)
MALRRALPALRPCIPRFVPLSTAPASREQPAAGPAAVPGGGSATAVRPPVPAVDFGNAQEAYRSRRTWELARSLLVLRLC
AWPALLARHEQLLYVSRKLLGQRLFNKLMKMTFYGHFVAGEDQESIQPLLRHYRAFGVSAILDYGVEEDLSPEEAEHKEM
ESCTSAAERDGSGTNKRDKQYQAHWAFGDRRNGVISARTYFYANEAKCDSHMETFLRCIEASGRVSDDGFIAIKLTALGR
PQFLLQFSEVLAKWRCFFHQMAVEQGQAGLAAMDTKLEVAVLQESVAKLGIASRAEIEDWFTAETLGVSGTMDLLDWSSL
IDSRTKLSKHLVVPNAQTGQLEPLLSRFTEEEELQMTRMLQRMDVLAKKATEMGVRLMVDAEQTYFQPAISRLTLEMQRK
FNVEKPLIFNTYQCYLKDAYDNVTLDVELAHREGWCFGAKLVRGAYLAQERARAAEIGYEDPINPTYEATNAMYHRCLDY
VLEELKHNAKAKVMVASHNEDTVRFALRRMEELGLHPADHRVYFGQLLGMCDQISFPLGQAGYPVYKYVPYGPVMEVLPY
LSRRALENSSLMKGTHRERQLLWLELLRRLRTGNLFHRPA*
Variant Samples
Additional References at PubMed
PMID:12217952   PMID:15662599   PMID:25741868   PMID:28492532  


Additional Information

Database Acc Id Source(s)
ClinVar RCV000004224 CLINVAR
  RCV000004225 CLINVAR
dbSNP (RS) rs2904552 CLINVAR
GWAS Catalog GCST90176332 GWAS Catalog
  GCST90178267 GWAS Catalog
  GCST90178269 GWAS Catalog
  GCST90178270 GWAS Catalog
  GCST90178271 GWAS Catalog
  GCST90178273 GWAS Catalog
  GCST90178477 GWAS Catalog
MedGen C0268529 CLINVAR
  C1833247 CLINVAR
NCBI Gene PRODH CLINVAR
OMIM 239500 CLINVAR
  600850 CLINVAR
  606810 CLINVAR
OMIM Allele 606810.0007 CLINVAR
SNOMED CT 61071003 CLINVAR