RGD:8599802 Rat Genome Database

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Variant: RGD:8599802 -  Homo sapiens

RGD ID: 8599802
RS ID: rs121912523
ClinVar ID: CV29430
Genic Status: GENIC
Type: SNV (SO:0001483) 
Associated Genes: LHCGR  STON1-GTF2A1L  
Reference Nucleotide: C
Variant Nucleotide: A
Position
Assembly Chr Position
GRCh37 2 48,915,301
GRCh38 2 48,688,162
JBrowse: View Region in Genome Browser (JBrowse)
Model



ClinVar Data
HGVS Name(s) Last Evaluated Molecular Consequence Clinical Significance Trait Synonyms
NC_000002.12:g.48688162G>T
NC_000002.11:g.48915301G>T
NP_000224.2:p.Cys545Ter
NM_000233.4:c.1635C>A
More...
12/31/2021 intron|intron variant|nonsense|stop-gain pathogenic|likely pathogenic Familial male-limited precocious puberty; Familial Testotoxicosis (subtype); Gonadotropin-independent familial sexual precocity; HYPERGONADOTROPIC HYPOGONADISM, MALE, DUE TO LHCGR DEFECT; LEYDIG CELL HYPOPLASIA WITH MALE PSEUDOHERMAPHRODITISM; LEYDIG CELL HYPOPLASIA, COMPLETE; Leydig cell hypoplasia, type 1; none provided; Pubertas Praecox; Testotoxicosis; TESTOTOXICOSIS, FAMILIAL
Disease Annotations     Click to see Annotation Detail View


Variant Details
Variant Transcripts
Gene Symbol:LHCGR
Accession:NM_000233
Location:EXON
Amino Acid Prediction: C to C (synonymous)
Amino Acid Position: 545
Amino Acid Sequence
(Calculated using NCBI transcript definition)
MKQRFSALQLLKLLLLLQPPLPRALREALCPEPCNCVPDGALRCPGPTAGLTRLSLAYLPVKVIPSQAFRGLNEVIKIEI
SQIDSLERIEANAFDNLLNLSEILIQNTKNLRYIEPGAFINLPRLKYLSICNTGIRKFPDVTKVFSSESNFILEICDNLH
ITTIPGNAFQGMNNESVTLKLYGNGFEEVQSHAFNGTTLTSLELKENVHLEKMHNGAFRGATGPKTLDISSTKLQALPSY
GLESIQRLIATSSYSLKKLPSRETFVNLLEATLTYPSHCCAFRNLPTKEQNFSHSISENFSKQCESTVRKVNNKTLYSSM
LAESELSGWDYEYGFCLPKTPRCAPEPDAFNPCEDIMGYDFLRVLIWLINILAIMGNMTVLFVLLTSRYKLTVPRFLMCN
LSFADFCMGLYLLLIASVDSQTKGQYYNHAIDWQTGSGCSTAGFFTVFASELSVYTLTVITLERWHTITYAIHLDQKLRL
RHAILIMLGGWLFSSLIAMLPLVGVSNYMKVSICFPMDVETTLSQVYILTILILNVVAFFIICACYIKIYFAVRNPELMA
TNKDTKIAKKMAILIFTDFTCMAPISFFAISAAFKVPLITVTNSKVLLVLFYPINSCANPFLYAIFTKTFQRDFFLLLSK
FGCCKRRAELYRRKDFSAYTSNCKNGFTGSNKPSQSTLKLSTLHCQGTALLDKTRYTEC*

Gene Symbol:LHCGR
Accession:XM_005264309
Location:EXON
Amino Acid Prediction: C to C (synonymous)
Amino Acid Position: 226
Amino Acid Sequence
(Calculated using NCBI transcript definition)
MLAESELSGWDYEYGFCLPKTPRCAPEPDAFNPCEDIMGYDFLRVLIWLINILAIMGNMTVLFVLLTSRYKLTVPRFLMC
NLSFADFCMGLYLLLIASVDSQTKGQYYNHAIDWQTGSGCSTAGFFTVFASELSVYTLTVITLERWHTITYAIHLDQKLR
LRHAILIMLGGWLFSSLIAMLPLVGVSNYMKVSICFPMDVETTLSQVYILTILILNVVAFFIICACYIKIYFAVRNPELM
ATNKDTKIAKKMAILIFTDFTCMAPISFFAISAAFKVPLITVTNSKVLLVLFYPINSCANPFLYAIFTKTFQRDFFLLLS
KFGCCKRRAELYRRKDFSAYTSNCKNGFTGSNKPSQSTLKLSTLHCQGTALLDKTRYTEC*

Gene Symbol:LHCGR
Accession:XM_006712015
Location:EXON
Amino Acid Prediction: C to C (synonymous)
Amino Acid Position: 235
Amino Acid Sequence
(Calculated using NCBI transcript definition)
MRQHQGYSSMLAESELSGWDYEYGFCLPKTPRCAPEPDAFNPCEDIMGYDFLRVLIWLINILAIMGNMTVLFVLLTSRYK
LTVPRFLMCNLSFADFCMGLYLLLIASVDSQTKGQYYNHAIDWQTGSGCSTAGFFTVFASELSVYTLTVITLERWHTITY
AIHLDQKLRLRHAILIMLGGWLFSSLIAMLPLVGVSNYMKVSICFPMDVETTLSQVYILTILILNVVAFFIICACYIKIY
FAVRNPELMATNKDTKIAKKMAILIFTDFTCMAPISFFAISAAFKVPLITVTNSKVLLVLFYPINSCANPFLYAIFTKTF
QRDFFLLLSKFGCCKRRAELYRRKDFSAYTSNCKNGFTGSNKPSQSTLKLSTLHCQGTALLDKTRYTEC*

Gene Symbol:LHCGR
Accession:XM_011532834
Location:EXON
Amino Acid Prediction: C to C (synonymous)
Amino Acid Position: 226
Amino Acid Sequence
(Calculated using NCBI transcript definition)
MLAESELSGWDYEYGFCLPKTPRCAPEPDAFNPCEDIMGYDFLRVLIWLINILAIMGNMTVLFVLLTSRYKLTVPRFLMC
NLSFADFCMGLYLLLIASVDSQTKGQYYNHAIDWQTGSGCSTAGFFTVFASELSVYTLTVITLERWHTITYAIHLDQKLR
LRHAILIMLGGWLFSSLIAMLPLVGVSNYMKVSICFPMDVETTLSQVYILTILILNVVAFFIICACYIKIYFAVRNPELM
ATNKDTKIAKKMAILIFTDFTCMAPISFFAISAAFKVPLITVTNSKVLLVLFYPINSCANPFLYAIFTKTFQRDFFLLLS
KFGCCKRRAELYRRKDFSAYTSNCKNGFTGSNKPSQSTLKLSTLHCQGTALLDKTRYTEC*

Gene Symbol:LHCGR
Accession:XM_017004090
Location:EXON
Amino Acid Prediction: C to C (synonymous)
Amino Acid Position: 333
Amino Acid Sequence
(Calculated using NCBI transcript definition)
MHNGAFRGATGPKTLDISSTKLQALPSYGLESIQRLIATSSYSLKKLPSRETFVNLLEATLTYPSHCCAFRNLPTKEQNF
SHSISENFSKQCESTVRKVNNKTLYSSMLAESELSGWDYEYGFCLPKTPRCAPEPDAFNPCEDIMGYDFLRVLIWLINIL
AIMGNMTVLFVLLTSRYKLTVPRFLMCNLSFADFCMGLYLLLIASVDSQTKGQYYNHAIDWQTGSGCSTAGFFTVFASEL
SVYTLTVITLERWHTITYAIHLDQKLRLRHAILIMLGGWLFSSLIAMLPLVGVSNYMKVSICFPMDVETTLSQVYILTIL
ILNVVAFFIICACYIKIYFAVRNPELMATNKDTKIAKKMAILIFTDFTCMAPISFFAISAAFKVPLITVTNSKVLLVLFY
PINSCANPFLYAIFTKTFQRDFFLLLSKFGCCKRRAELYRRKDFSAYTSNCKNGFTGSNKPSQSTLKLSTLHCQGTALLD
KTRYTEC*

Gene Symbol:LHCGR
Accession:XM_047444293
Location:EXON
Amino Acid Prediction: C to C (synonymous)
Amino Acid Position: 458
Amino Acid Sequence
(Calculated using NCBI transcript definition)
MKQRFSALQLLKLLLLLQPPLPRALREALCPEPCNCVPDGALRCPGPTAGLTRLSLAYLPVKVIPSQAFRGLNEVIKILI
QNTKNLRYIEPGAFINLPRLKYLSICNTGIRKFPDVTKVFSSESNFILEICDNLHITTIPGNAFQGMNNESVTLKLYGNG
FEEVQSHAFNGTTLTSLELKENVHLEKMHNGAFRGATGPKTLQNFSHSISENFSKQCESTVRKVNNKTLYSSMLAESELS
GWDYEYGFCLPKTPRCAPEPDAFNPCEDIMGYDFLRVLIWLINILAIMGNMTVLFVLLTSRYKLTVPRFLMCNLSFADFC
MGLYLLLIASVDSQTKGQYYNHAIDWQTGSGCSTAGFFTVFASELSVYTLTVITLERWHTITYAIHLDQKLRLRHAILIM
LGGWLFSSLIAMLPLVGVSNYMKVSICFPMDVETTLSQVYILTILILNVVAFFIICACYIKIYFAVRNPELMATNKDTKI
AKKMAILIFTDFTCMAPISFFAISAAFKVPLITVTNSKVLLVLFYPINSCANPFLYAIFTKTFQRDFFLLLSKFGCCKRR
AELYRRKDFSAYTSNCKNGFTGSNKPSQSTLKLSTLHCQGTALLDKTRYTEC*

Gene Symbol:LHCGR
Accession:XM_047444291
Location:EXON
Amino Acid Prediction: C to C (synonymous)
Amino Acid Position: 520
Amino Acid Sequence
(Calculated using NCBI transcript definition)
MKQRFSALQLLKLLLLLQPPLPRALREALCPEPCNCVPDGALRCPGPTAGLTRLSLAYLPVKVIPSQAFRGLNEVIKILI
QNTKNLRYIEPGAFINLPRLKYLSICNTGIRKFPDVTKVFSSESNFILEICDNLHITTIPGNAFQGMNNESVTLKLYGNG
FEEVQSHAFNGTTLTSLELKENVHLEKMHNGAFRGATGPKTLDISSTKLQALPSYGLESIQRLIATSSYSLKKLPSRETF
VNLLEATLTYPSHCCAFRNLPTKEQNFSHSISENFSKQCESTVRKVNNKTLYSSMLAESELSGWDYEYGFCLPKTPRCAP
EPDAFNPCEDIMGYDFLRVLIWLINILAIMGNMTVLFVLLTSRYKLTVPRFLMCNLSFADFCMGLYLLLIASVDSQTKGQ
YYNHAIDWQTGSGCSTAGFFTVFASELSVYTLTVITLERWHTITYAIHLDQKLRLRHAILIMLGGWLFSSLIAMLPLVGV
SNYMKVSICFPMDVETTLSQVYILTILILNVVAFFIICACYIKIYFAVRNPELMATNKDTKIAKKMAILIFTDFTCMAPI
SFFAISAAFKVPLITVTNSKVLLVLFYPINSCANPFLYAIFTKTFQRDFFLLLSKFGCCKRRAELYRRKDFSAYTSNCKN
GFTGSNKPSQSTLKLSTLHCQGTALLDKTRYTEC*

Gene Symbol:LHCGR
Accession:XM_047444292
Location:EXON
Amino Acid Prediction: C to C (synonymous)
Amino Acid Position: 483
Amino Acid Sequence
(Calculated using NCBI transcript definition)
MKQRFSALQLLKLLLLLQPPLPRALREALCPEPCNCVPDGALRCPGPTAGLTRLSLAYLPVKVIPSQAFRGLNEVIKIEI
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

Variant Samples
Additional References at PubMed
PMID:7581384   PMID:9817592   PMID:25741868   PMID:26246498   PMID:27016457   PMID:28492532  


Additional Information

Database Acc Id Source(s)
ClinVar RCV000015469 CLINVAR
  RCV002490374 CLINVAR
  RCV003546456 CLINVAR
dbSNP (RS) rs121912523 CLINVAR
MedGen C0266432 CLINVAR
  C3661900 CLINVAR
NCBI Gene LHCGR CLINVAR
  STON1-GTF2A1L CLINVAR
OMIM 152790 CLINVAR
  176410 CLINVAR
  238320 CLINVAR
OMIM Allele 152790.0007 CLINVAR
SNOMED CT 56212008 CLINVAR