RGD:28889266 Rat Genome Database

Variant: RGD:28889266 - Homo sapiens

RGD ID:

28889266

RS ID:

rs577862345

ClinVar ID:

CV862021

Genic Status:

GENIC

Type:

SNV (SO:0001483)

Associated Genes:

VANGL1

Reference Nucleotide:

Variant Nucleotide:

Position

Assembly	Chr	Position
GRCh37	1	116,206,689
GRCh38	1	115,664,068

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	Trait Synonyms
NC_000001.10:g.116206689C>T NM_138959.2:c.612C>T NM_001172411.2:c.606C>T NG_016548.1:g.27116C>T More...	01/13/2018	synonymous variant	uncertain significance	Neural tube defects

Disease Annotations Click to see Annotation Detail View

caudal regression syndrome (IAGP)

neural tube defect (IAGP)

Phenotype Annotations Click to see Annotation Detail View

Human Phenotype

Neural tube defect (IAGP)

Variant Details

Variant Transcripts

Gene Symbol:	VANGL1
Accession:	NM_001172412
Location:	EXON
Amino Acid Prediction:	Y to Y (synonymous)
Amino Acid Position:	204

Amino Acid Sequence (Calculated using NCBI transcript definition)
MDTESTYSGYSYYSSHSKKSHRQGERTRERHKSPRNKDGRGSEKSVTIQPPTGEPLLGNDSTRTEEVQDDNWGETTTAIT GTSEHSISQEDIARISKDMEDSVGLDCKRYLGLTVASFLGLLVFLTPIAFILLPPILWRDELEPCGTICEGLFISMAFKL LILLIGTWALFFRKRRADMPRVFVFRALLLVLIFLFVVSYWLFYGVRILDSRDRNYQGIVQYAVSLVDALLFIHYLAIVL LELRQLQPMFTLQVVRSTDGESRFYSLGHLSIQRAALVVLENYYKDFTIYNPNLLTASKFRAAKHMAGLKVYNVDGPSNN ATGQSRAMIAAAARRRDSSHNELYYEEAEHERRVKKRKARLVVAVEEAFIHIQRLQAEEQQKAPGEVMDPREAAQAIFPS MARALQKYLRITRQQNYHSMESILQHLAFCITNGMTPKAFLERYLSAGPTLQYDKDRWLSTQWRLVSDEAVTNGLRDGIV FVLKCLDFSLVVNVKKIPFIILSEEFIDPKSHKFVLRLQSETSV*

Gene Symbol:	VANGL1
Accession:	NM_001172411
Location:	EXON
Amino Acid Prediction:	Y to Y (synonymous)
Amino Acid Position:	202

Amino Acid Sequence (Calculated using NCBI transcript definition)
MDTESTYSGYSYYSSHSKKSHRQGERTRERHKSPRNKDGRGSEKSVTIQPPTGEPLLGNDSTRTEEDDNWGETTTAITGT SEHSISQEDIARISKDMEDSVGLDCKRYLGLTVASFLGLLVFLTPIAFILLPPILWRDELEPCGTICEGLFISMAFKLLI LLIGTWALFFRKRRADMPRVFVFRALLLVLIFLFVVSYWLFYGVRILDSRDRNYQGIVQYAVSLVDALLFIHYLAIVLLE LRQLQPMFTLQVVRSTDGESRFYSLGHLSIQRAALVVLENYYKDFTIYNPNLLTASKFRAAKHMAGLKVYNVDGPSNNAT GQSRAMIAAAARRRDSSHNELYYEEAEHERRVKKRKARLVVAVEEAFIHIQRLQAEEQQKAPGEVMDPREAAQAIFPSMA RALQKYLRITRQQNYHSMESILQHLAFCITNGMTPKAFLERYLSAGPTLQYDKDRWLSTQWRLVSDEAVTNGLRDGIVFV LKCLDFSLVVNVKKIPFIILSEEFIDPKSHKFVLRLQSETSV*

Gene Symbol:	VANGL1
Accession:	NM_138959
Location:	EXON
Amino Acid Prediction:	Y to Y (synonymous)
Amino Acid Position:	204

Amino Acid Sequence (Calculated using NCBI transcript definition)
MDTESTYSGYSYYSSHSKKSHRQGERTRERHKSPRNKDGRGSEKSVTIQPPTGEPLLGNDSTRTEEVQDDNWGETTTAIT GTSEHSISQEDIARISKDMEDSVGLDCKRYLGLTVASFLGLLVFLTPIAFILLPPILWRDELEPCGTICEGLFISMAFKL LILLIGTWALFFRKRRADMPRVFVFRALLLVLIFLFVVSYWLFYGVRILDSRDRNYQGIVQYAVSLVDALLFIHYLAIVL LELRQLQPMFTLQVVRSTDGESRFYSLGHLSIQRAALVVLENYYKDFTIYNPNLLTASKFRAAKHMAGLKVYNVDGPSNN ATGQSRAMIAAAARRRDSSHNELYYEEAEHERRVKKRKARLVVAVEEAFIHIQRLQAEEQQKAPGEVMDPREAAQAIFPS MARALQKYLRITRQQNYHSMESILQHLAFCITNGMTPKAFLERYLSAGPTLQYDKDRWLSTQWRLVSDEAVTNGLRDGIV FVLKCLDFSLVVNVKKIPFIILSEEFIDPKSHKFVLRLQSETSV*

Variant Samples

ClinVar GRCh37

ClinVar GRCh38

Additional Information

External Database Links

Database	Acc Id	Source(s)
ClinVar	RCV001099364	CLINVAR
	RCV001099365	CLINVAR
dbSNP (RS)	rs577862345	CLINVAR
MedGen	C0027794	CLINVAR
	C1838568	CLINVAR
NCBI Gene	VANGL1	CLINVAR
OMIM	182940	CLINVAR
	600145	CLINVAR
	610132	CLINVAR
SNOMED CT	253098009	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:28889266 - Homo sapiens

Imported Disease Annotations - ClinVar

Imported Human Phenotype Annotations - ClinVar

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Variant: RGD:28889266 - Homo sapiens

Imported Disease Annotations - ClinVar

Imported Human Phenotype Annotations - ClinVar