RGD:11582988 Rat Genome Database

Variant: RGD:11582988 - Homo sapiens

RGD ID:

11582988

RS ID:

rs114320052

ClinVar ID:

CV289855

Genic Status:

GENIC

Type:

SNV (SO:0001483)

Associated Genes:

LHCGR STON1-GTF2A1L

Reference Nucleotide:

Variant Nucleotide:

Position

Assembly	Chr	Position
GRCh37	2	48,915,576
GRCh38	2	48,688,437

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

ClinVar Data

HGVS Name(s)	Last Evaluated	Molecular Consequence	Clinical Significance	Age of Onset	Prevalence	Trait Synonyms
NC_000002.12:g.48688437C>T NC_000002.11:g.48915576C>T NP_000224.2:p.Val454Ile NM_000233.4:c.1360G>A More...	07/31/2018	intron variant\|missense variant	benign\|likely benign\|conflicting interpretations of pathogenicity\|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; none provided; Pubertas Praecox; Testotoxicosis; TESTOTOXICOSIS, FAMILIAL

Disease Annotations Click to see Annotation Detail View

familial male-limited precocious puberty (IAGP)

hypogonadism (IAGP)

Leydig cell hypoplasia (IAGP)

Phenotype Annotations Click to see Annotation Detail View

Human Phenotype

Hypergonadotropic hypogonadism (IAGP)

Variant Details

Variant Transcripts

Gene Symbol:	LHCGR
Accession:	XM_006712015
Location:	EXON
Amino Acid Prediction:	V to F (nonsynonymous)
Amino Acid Position:	144

Amino Acid Sequence (Calculated using NCBI transcript definition)
MRQHQGYSSMLAESELSGWDYEYGFCLPKTPRCAPEPDAFNPCEDIMGYDFLRVLIWLINILAIMGNMTVLFVLLTSRYK LTVPRFLMCNLSFADFCMGLYLLLIASVDSQTKGQYYNHAIDWQTGSGCSTAGFFTVFASELSFYTLTVITLERWHTITY AIHLDQKLRLRHAILIMLGGWLFSSLIAMLPLVGVSNYMKVSICFPMDVETTLSQVYILTILILNVVAFFIICACYIKIY FAVRNPELMATNKDTKIAKKMAILIFTDFTCMAPISFFAISAAFKVPLITVTNSKVLLVLFYPINSCANPFLYAIFTKTF QRDFFLLLSKFGCCKRRAELYRRKDFSAYTSNCKNGFTGSNKPSQSTLKLSTLHCQGTALLDKTRYTEC*

Gene Symbol:	LHCGR
Accession:	XM_047444292
Location:	EXON
Amino Acid Prediction:	V to F (nonsynonymous)
Amino Acid Position:	392

Amino Acid Sequence (Calculated using NCBI transcript definition)
MKQRFSALQLLKLLLLLQPPLPRALREALCPEPCNCVPDGALRCPGPTAGLTRLSLAYLPVKVIPSQAFRGLNEVIKIEI SQIDSLERIEANAFDNLLNLSEILIQNTKNLRYIEPGAFINLPRLKYLSICNTGIRKFPDVTKVFSSESNFILEICDNLH ITTIPGNAFQGMNNESVTLKLYGNGFEEVQSHAFNGTTLTSLELKENVHLEKMHNGAFRGATGPKTLQNFSHSISENFSK QCESTVRKVNNKTLYSSMLAESELSGWDYEYGFCLPKTPRCAPEPDAFNPCEDIMGYDFLRVLIWLINILAIMGNMTVLF VLLTSRYKLTVPRFLMCNLSFADFCMGLYLLLIASVDSQTKGQYYNHAIDWQTGSGCSTAGFFTVFASELSFYTLTVITL ERWHTITYAIHLDQKLRLRHAILIMLGGWLFSSLIAMLPLVGVSNYMKVSICFPMDVETTLSQVYILTILILNVVAFFII CACYIKIYFAVRNPELMATNKDTKIAKKMAILIFTDFTCMAPISFFAISAAFKVPLITVTNSKVLLVLFYPINSCANPFL YAIFTKTFQRDFFLLLSKFGCCKRRAELYRRKDFSAYTSNCKNGFTGSNKPSQSTLKLSTLHCQGTALLDKTRYTEC*

Gene Symbol:	LHCGR
Accession:	XM_005264309
Location:	EXON
Amino Acid Prediction:	V to F (nonsynonymous)
Amino Acid Position:	135

Amino Acid Sequence (Calculated using NCBI transcript definition)
MLAESELSGWDYEYGFCLPKTPRCAPEPDAFNPCEDIMGYDFLRVLIWLINILAIMGNMTVLFVLLTSRYKLTVPRFLMC NLSFADFCMGLYLLLIASVDSQTKGQYYNHAIDWQTGSGCSTAGFFTVFASELSFYTLTVITLERWHTITYAIHLDQKLR LRHAILIMLGGWLFSSLIAMLPLVGVSNYMKVSICFPMDVETTLSQVYILTILILNVVAFFIICACYIKIYFAVRNPELM ATNKDTKIAKKMAILIFTDFTCMAPISFFAISAAFKVPLITVTNSKVLLVLFYPINSCANPFLYAIFTKTFQRDFFLLLS KFGCCKRRAELYRRKDFSAYTSNCKNGFTGSNKPSQSTLKLSTLHCQGTALLDKTRYTEC*

Gene Symbol:	LHCGR
Accession:	XM_047444291
Location:	EXON
Amino Acid Prediction:	V to F (nonsynonymous)
Amino Acid Position:	429

Amino Acid Sequence (Calculated using NCBI transcript definition)
MKQRFSALQLLKLLLLLQPPLPRALREALCPEPCNCVPDGALRCPGPTAGLTRLSLAYLPVKVIPSQAFRGLNEVIKILI QNTKNLRYIEPGAFINLPRLKYLSICNTGIRKFPDVTKVFSSESNFILEICDNLHITTIPGNAFQGMNNESVTLKLYGNG FEEVQSHAFNGTTLTSLELKENVHLEKMHNGAFRGATGPKTLDISSTKLQALPSYGLESIQRLIATSSYSLKKLPSRETF VNLLEATLTYPSHCCAFRNLPTKEQNFSHSISENFSKQCESTVRKVNNKTLYSSMLAESELSGWDYEYGFCLPKTPRCAP EPDAFNPCEDIMGYDFLRVLIWLINILAIMGNMTVLFVLLTSRYKLTVPRFLMCNLSFADFCMGLYLLLIASVDSQTKGQ YYNHAIDWQTGSGCSTAGFFTVFASELSFYTLTVITLERWHTITYAIHLDQKLRLRHAILIMLGGWLFSSLIAMLPLVGV SNYMKVSICFPMDVETTLSQVYILTILILNVVAFFIICACYIKIYFAVRNPELMATNKDTKIAKKMAILIFTDFTCMAPI SFFAISAAFKVPLITVTNSKVLLVLFYPINSCANPFLYAIFTKTFQRDFFLLLSKFGCCKRRAELYRRKDFSAYTSNCKN GFTGSNKPSQSTLKLSTLHCQGTALLDKTRYTEC*

Gene Symbol:	LHCGR
Accession:	XM_017004090
Location:	EXON
Amino Acid Prediction:	V to F (nonsynonymous)
Amino Acid Position:	242

Amino Acid Sequence (Calculated using NCBI transcript definition)
MHNGAFRGATGPKTLDISSTKLQALPSYGLESIQRLIATSSYSLKKLPSRETFVNLLEATLTYPSHCCAFRNLPTKEQNF SHSISENFSKQCESTVRKVNNKTLYSSMLAESELSGWDYEYGFCLPKTPRCAPEPDAFNPCEDIMGYDFLRVLIWLINIL AIMGNMTVLFVLLTSRYKLTVPRFLMCNLSFADFCMGLYLLLIASVDSQTKGQYYNHAIDWQTGSGCSTAGFFTVFASEL SFYTLTVITLERWHTITYAIHLDQKLRLRHAILIMLGGWLFSSLIAMLPLVGVSNYMKVSICFPMDVETTLSQVYILTIL ILNVVAFFIICACYIKIYFAVRNPELMATNKDTKIAKKMAILIFTDFTCMAPISFFAISAAFKVPLITVTNSKVLLVLFY PINSCANPFLYAIFTKTFQRDFFLLLSKFGCCKRRAELYRRKDFSAYTSNCKNGFTGSNKPSQSTLKLSTLHCQGTALLD KTRYTEC*

Gene Symbol:	LHCGR
Accession:	XM_047444293
Location:	EXON
Amino Acid Prediction:	V to F (nonsynonymous)
Amino Acid Position:	367

Amino Acid Sequence (Calculated using NCBI transcript definition)
MKQRFSALQLLKLLLLLQPPLPRALREALCPEPCNCVPDGALRCPGPTAGLTRLSLAYLPVKVIPSQAFRGLNEVIKILI QNTKNLRYIEPGAFINLPRLKYLSICNTGIRKFPDVTKVFSSESNFILEICDNLHITTIPGNAFQGMNNESVTLKLYGNG FEEVQSHAFNGTTLTSLELKENVHLEKMHNGAFRGATGPKTLQNFSHSISENFSKQCESTVRKVNNKTLYSSMLAESELS GWDYEYGFCLPKTPRCAPEPDAFNPCEDIMGYDFLRVLIWLINILAIMGNMTVLFVLLTSRYKLTVPRFLMCNLSFADFC MGLYLLLIASVDSQTKGQYYNHAIDWQTGSGCSTAGFFTVFASELSFYTLTVITLERWHTITYAIHLDQKLRLRHAILIM LGGWLFSSLIAMLPLVGVSNYMKVSICFPMDVETTLSQVYILTILILNVVAFFIICACYIKIYFAVRNPELMATNKDTKI AKKMAILIFTDFTCMAPISFFAISAAFKVPLITVTNSKVLLVLFYPINSCANPFLYAIFTKTFQRDFFLLLSKFGCCKRR AELYRRKDFSAYTSNCKNGFTGSNKPSQSTLKLSTLHCQGTALLDKTRYTEC*

Gene Symbol:	LHCGR
Accession:	XM_011532834
Location:	EXON
Amino Acid Prediction:	V to F (nonsynonymous)
Amino Acid Position:	135

Amino Acid Sequence (Calculated using NCBI transcript definition)
MLAESELSGWDYEYGFCLPKTPRCAPEPDAFNPCEDIMGYDFLRVLIWLINILAIMGNMTVLFVLLTSRYKLTVPRFLMC NLSFADFCMGLYLLLIASVDSQTKGQYYNHAIDWQTGSGCSTAGFFTVFASELSFYTLTVITLERWHTITYAIHLDQKLR LRHAILIMLGGWLFSSLIAMLPLVGVSNYMKVSICFPMDVETTLSQVYILTILILNVVAFFIICACYIKIYFAVRNPELM ATNKDTKIAKKMAILIFTDFTCMAPISFFAISAAFKVPLITVTNSKVLLVLFYPINSCANPFLYAIFTKTFQRDFFLLLS KFGCCKRRAELYRRKDFSAYTSNCKNGFTGSNKPSQSTLKLSTLHCQGTALLDKTRYTEC*

Gene Symbol:	LHCGR
Accession:	NM_000233
Location:	EXON
Amino Acid Prediction:	V to F (nonsynonymous)
Amino Acid Position:	454

Amino Acid Sequence (Calculated using NCBI transcript definition)
MKQRFSALQLLKLLLLLQPPLPRALREALCPEPCNCVPDGALRCPGPTAGLTRLSLAYLPVKVIPSQAFRGLNEVIKIEI SQIDSLERIEANAFDNLLNLSEILIQNTKNLRYIEPGAFINLPRLKYLSICNTGIRKFPDVTKVFSSESNFILEICDNLH ITTIPGNAFQGMNNESVTLKLYGNGFEEVQSHAFNGTTLTSLELKENVHLEKMHNGAFRGATGPKTLDISSTKLQALPSY GLESIQRLIATSSYSLKKLPSRETFVNLLEATLTYPSHCCAFRNLPTKEQNFSHSISENFSKQCESTVRKVNNKTLYSSM LAESELSGWDYEYGFCLPKTPRCAPEPDAFNPCEDIMGYDFLRVLIWLINILAIMGNMTVLFVLLTSRYKLTVPRFLMCN LSFADFCMGLYLLLIASVDSQTKGQYYNHAIDWQTGSGCSTAGFFTVFASELSFYTLTVITLERWHTITYAIHLDQKLRL RHAILIMLGGWLFSSLIAMLPLVGVSNYMKVSICFPMDVETTLSQVYILTILILNVVAFFIICACYIKIYFAVRNPELMA TNKDTKIAKKMAILIFTDFTCMAPISFFAISAAFKVPLITVTNSKVLLVLFYPINSCANPFLYAIFTKTFQRDFFLLLSK FGCCKRRAELYRRKDFSAYTSNCKNGFTGSNKPSQSTLKLSTLHCQGTALLDKTRYTEC*

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

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

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

Variant Samples

ClinVar GRCh37

ClinVar GRCh38

Additional References at PubMed

PMID:28492532

Additional Information

External Database Links

Database	Acc Id	Source(s)
ClinVar	RCV000263657	CLINVAR
	RCV000318790	CLINVAR
	RCV000373581	CLINVAR
	RCV000731559	CLINVAR
dbSNP (RS)	rs114320052	CLINVAR
MedGen	C0266432	CLINVAR
	C0342549	CLINVAR
	C0948896	CLINVAR
	C3661900	CLINVAR
NCBI Gene	LHCGR	CLINVAR
	STON1-GTF2A1L	CLINVAR
OMIM	152790	CLINVAR
	176410	CLINVAR
	238320	CLINVAR
SNOMED CT	237818003	CLINVAR
	56212008	CLINVAR

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Variant: RGD:11582988 - Homo sapiens

Imported Disease Annotations - ClinVar

Imported Human Phenotype Annotations - ClinVar

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Variant: RGD:11582988 - Homo sapiens

Imported Disease Annotations - ClinVar

Imported Human Phenotype Annotations - ClinVar