RGD:11585294 Rat Genome Database

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Variant: RGD:11585294 -  Homo sapiens

RGD ID: 11585294
RS ID: rs780848944
ClinVar ID: CV289860
Genic Status: GENIC
Type: SNV (SO:0001483) 
Associated Genes: LHCGR  STON1-GTF2A1L  
Reference Nucleotide: G
Variant Nucleotide: A
Position
Assembly Chr Position
GRCh37 2 48,982,757
GRCh38 2 48,755,618
JBrowse: View Region in Genome Browser (JBrowse)
Model



ClinVar Data
HGVS Name(s) Last Evaluated Molecular Consequence Clinical Significance Age of Onset Prevalence Trait Synonyms
NC_000002.12:g.48755618C>T
NC_000002.11:g.48982757C>T
NP_000224.2:p.Gln18=
NM_000233.4:c.54G>A
More... 		04/16/2019 intron variant|synonymous variant likely benign|uncertain significance childhood <1 / 1 000 000 Familial male-limited precocious puberty; Familial Testotoxicosis (subtype); HYPERGONADOTROPIC HYPOGONADISM, MALE, DUE TO LHCGR DEFECT; LEYDIG CELL HYPOPLASIA WITH MALE PSEUDOHERMAPHRODITISM; LEYDIG CELL HYPOPLASIA, COMPLETE; Leydig cell hypoplasia, type 1; Pubertas Praecox; Testotoxicosis; TESTOTOXICOSIS, FAMILIAL
Disease Annotations     Click to see Annotation Detail View

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype

Variant Details
Variant Transcripts
Gene Symbol:LHCGR
Accession:NM_000233
Location:EXON
Amino Acid Prediction: Q to H (nonsynonymous)
Amino Acid Position: 18
Amino Acid Sequence
(Calculated using NCBI transcript definition)
MKQRFSALQLLKLLLLLHPPLPRALREALCPEPCNCVPDGALRCPGPTAGLTRLSLAYLPVKVIPSQAFRGLNEVIKIEI
SQIDSLERIEANAFDNLLNLSEILIQNTKNLRYIEPGAFINLPRLKYLSICNTGIRKFPDVTKVFSSESNFILEICDNLH
ITTIPGNAFQGMNNESVTLKLYGNGFEEVQSHAFNGTTLTSLELKENVHLEKMHNGAFRGATGPKTLDISSTKLQALPSY
GLESIQRLIATSSYSLKKLPSRETFVNLLEATLTYPSHCCAFRNLPTKEQNFSHSISENFSKQCESTVRKVNNKTLYSSM
LAESELSGWDYEYGFCLPKTPRCAPEPDAFNPCEDIMGYDFLRVLIWLINILAIMGNMTVLFVLLTSRYKLTVPRFLMCN
LSFADFCMGLYLLLIASVDSQTKGQYYNHAIDWQTGSGCSTAGFFTVFASELSVYTLTVITLERWHTITYAIHLDQKLRL
RHAILIMLGGWLFSSLIAMLPLVGVSNYMKVSICFPMDVETTLSQVYILTILILNVVAFFIICACYIKIYFAVRNPELMA
TNKDTKIAKKMAILIFTDFTCMAPISFFAISAAFKVPLITVTNSKVLLVLFYPINSCANPFLYAIFTKTFQRDFFLLLSK
FGCCKRRAELYRRKDFSAYTSNCKNGFTGSNKPSQSTLKLSTLHCQGTALLDKTRYTEC*

Gene Symbol:LHCGR
Accession:XM_047444293
Location:EXON
Amino Acid Prediction: Q to H (nonsynonymous)
Amino Acid Position: 18
Amino Acid Sequence
(Calculated using NCBI transcript definition)
MKQRFSALQLLKLLLLLHPPLPRALREALCPEPCNCVPDGALRCPGPTAGLTRLSLAYLPVKVIPSQAFRGLNEVIKILI
QNTKNLRYIEPGAFINLPRLKYLSICNTGIRKFPDVTKVFSSESNFILEICDNLHITTIPGNAFQGMNNESVTLKLYGNG
FEEVQSHAFNGTTLTSLELKENVHLEKMHNGAFRGATGPKTLQNFSHSISENFSKQCESTVRKVNNKTLYSSMLAESELS
GWDYEYGFCLPKTPRCAPEPDAFNPCEDIMGYDFLRVLIWLINILAIMGNMTVLFVLLTSRYKLTVPRFLMCNLSFADFC
MGLYLLLIASVDSQTKGQYYNHAIDWQTGSGCSTAGFFTVFASELSVYTLTVITLERWHTITYAIHLDQKLRLRHAILIM
LGGWLFSSLIAMLPLVGVSNYMKVSICFPMDVETTLSQVYILTILILNVVAFFIICACYIKIYFAVRNPELMATNKDTKI
AKKMAILIFTDFTCMAPISFFAISAAFKVPLITVTNSKVLLVLFYPINSCANPFLYAIFTKTFQRDFFLLLSKFGCCKRR
AELYRRKDFSAYTSNCKNGFTGSNKPSQSTLKLSTLHCQGTALLDKTRYTEC*

Gene Symbol:LHCGR
Accession:XM_047444291
Location:EXON
Amino Acid Prediction: Q to H (nonsynonymous)
Amino Acid Position: 18
Amino Acid Sequence
(Calculated using NCBI transcript definition)
MKQRFSALQLLKLLLLLHPPLPRALREALCPEPCNCVPDGALRCPGPTAGLTRLSLAYLPVKVIPSQAFRGLNEVIKILI
QNTKNLRYIEPGAFINLPRLKYLSICNTGIRKFPDVTKVFSSESNFILEICDNLHITTIPGNAFQGMNNESVTLKLYGNG
FEEVQSHAFNGTTLTSLELKENVHLEKMHNGAFRGATGPKTLDISSTKLQALPSYGLESIQRLIATSSYSLKKLPSRETF
VNLLEATLTYPSHCCAFRNLPTKEQNFSHSISENFSKQCESTVRKVNNKTLYSSMLAESELSGWDYEYGFCLPKTPRCAP
EPDAFNPCEDIMGYDFLRVLIWLINILAIMGNMTVLFVLLTSRYKLTVPRFLMCNLSFADFCMGLYLLLIASVDSQTKGQ
YYNHAIDWQTGSGCSTAGFFTVFASELSVYTLTVITLERWHTITYAIHLDQKLRLRHAILIMLGGWLFSSLIAMLPLVGV
SNYMKVSICFPMDVETTLSQVYILTILILNVVAFFIICACYIKIYFAVRNPELMATNKDTKIAKKMAILIFTDFTCMAPI
SFFAISAAFKVPLITVTNSKVLLVLFYPINSCANPFLYAIFTKTFQRDFFLLLSKFGCCKRRAELYRRKDFSAYTSNCKN
GFTGSNKPSQSTLKLSTLHCQGTALLDKTRYTEC*

Gene Symbol:LHCGR
Accession:XM_047444292
Location:EXON
Amino Acid Prediction: Q to H (nonsynonymous)
Amino Acid Position: 18
Amino Acid Sequence
(Calculated using NCBI transcript definition)
MKQRFSALQLLKLLLLLHPPLPRALREALCPEPCNCVPDGALRCPGPTAGLTRLSLAYLPVKVIPSQAFRGLNEVIKIEI
SQIDSLERIEANAFDNLLNLSEILIQNTKNLRYIEPGAFINLPRLKYLSICNTGIRKFPDVTKVFSSESNFILEICDNLH
ITTIPGNAFQGMNNESVTLKLYGNGFEEVQSHAFNGTTLTSLELKENVHLEKMHNGAFRGATGPKTLQNFSHSISENFSK
QCESTVRKVNNKTLYSSMLAESELSGWDYEYGFCLPKTPRCAPEPDAFNPCEDIMGYDFLRVLIWLINILAIMGNMTVLF
VLLTSRYKLTVPRFLMCNLSFADFCMGLYLLLIASVDSQTKGQYYNHAIDWQTGSGCSTAGFFTVFASELSVYTLTVITL
ERWHTITYAIHLDQKLRLRHAILIMLGGWLFSSLIAMLPLVGVSNYMKVSICFPMDVETTLSQVYILTILILNVVAFFII
CACYIKIYFAVRNPELMATNKDTKIAKKMAILIFTDFTCMAPISFFAISAAFKVPLITVTNSKVLLVLFYPINSCANPFL
YAIFTKTFQRDFFLLLSKFGCCKRRAELYRRKDFSAYTSNCKNGFTGSNKPSQSTLKLSTLHCQGTALLDKTRYTEC*

Gene Symbol:STON1-GTF2A1L
Accession:NM_172311
Location:INTRON

Gene Symbol:STON1-GTF2A1L
Accession:NM_001198593
Location:INTRON

Gene Symbol:STON1-GTF2A1L
Accession:NM_001198594
Location:INTRON

Gene Symbol:LHCGR
Accession:XM_005264309
Location:INTRON

Gene Symbol:LHCGR
Accession:XM_006712015
Location:INTRON

Gene Symbol:LHCGR
Accession:XM_011532834
Location:INTRON

Gene Symbol:LHCGR
Accession:XM_017004090
Location:INTRON

Variant Samples
Additional References at PubMed
PMID:25741868  


Additional Information

Database Acc Id Source(s)
ClinVar RCV000280149 CLINVAR
  RCV000335238 CLINVAR
  RCV000374643 CLINVAR
  RCV003972424 CLINVAR
dbSNP (RS) rs780848944 CLINVAR
MedGen C0266432 CLINVAR
  C0342549 CLINVAR
  C0948896 CLINVAR
NCBI Gene LHCGR CLINVAR
  STON1-GTF2A1L CLINVAR
OMIM 152790 CLINVAR
  176410 CLINVAR
  238320 CLINVAR
SNOMED CT 237818003 CLINVAR
  56212008 CLINVAR