RGD:13792209 Rat Genome Database

Variant: RGD:13792209 - Homo sapiens

RGD ID:

13792209

RS ID:

rs200735968

ClinVar ID:

CV549170

Genic Status:

GENIC

Type:

SNV (SO:0001483)

Associated Genes:

SCO2 TYMP

Reference Nucleotide:

Variant Nucleotide:

Position

Assembly	Chr	Position
GRCh37	22	50,964,207
GRCh38	22	50,525,778

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
NM_001113755.3:c.1441C>T NM_001113756.3:c.1441C>T NP_001107227.1:p.Gln481Ter NP_001107228.1:p.Gln481Ter More...	08/01/2017	intron variant\|nonsense	uncertain significance	AllHighlyPenetrant; Mitochondrial DNA depletion syndrome 1 (MNGIE type); Mitochondrial DNA Depletion Syndrome, MNGIE Form; Mitochondrial neurogastrointestinal encephalomyopathy syndrome; MITOCHONDRIAL NEUROGASTROINTESTINAL ENCEPHALOPATHY SYNDROME, TYMP-RELATED; MNGIE, TYMP-RELATED; none provided; POLIP SYNDROME; POLYNEUROPATHY, OPHTHALMOPLEGIA, LEUKOENCEPHALOPATHY, AND INTESTINAL PSEUDOOBSTRUCTION

Disease Annotations Click to see Annotation Detail View

mitochondrial DNA depletion syndrome 1 (IAGP)

Variant Details

Variant Transcripts

Gene Symbol:	SCO2
Accession:	NM_001169110
Location:	5UTRS;INTRON

Gene Symbol:	SCO2
Accession:	NM_001169109
Location:	5UTRS;INTRON

Gene Symbol:	TYMP
Accession:	NM_001257988
Location:	EXON
Amino Acid Prediction:	Q to K (nonsynonymous)
Amino Acid Position:	481

Amino Acid Sequence (Calculated using NCBI transcript definition)
MAALMTPGTGAPPAPGDFSGEGSQGLPDPSPEPKQLPELIRMKRDGGRLSEADIRGFVAAVVNGSAQGAQIGAMLMAIRL RGMDLEETSVLTQALAQSGQQLEWPEAWRQQLVDKHSTGGVGDKVSLVLAPALAACGCKVPMISGRGLGHTGGTLDKLES IPGFNVIQSPEQMQVLLDQAGCCIVGQSEQLVPADGILYAARDVTATVDSLPLITASILSKKLVEGLSALVVDVKFGGAA VFPNQEQARELAKTLVGVGASLGLRVAAALTAMDKPLGRCVGHALEVEEALLCMDGAGPPDLRDLVTTLGGALLWLSGHA GTQAQGAARVAAALDDGSALGRFERMLAAQGVDPGLARALCSGSPAERRQLLPRAREQEELLAPADGTVELVRALPLALV LHELGAGRSRAGEPLRLGVGAELLVDVGQRLRRGTPWLRVHRDGPALSGPQSRALQEALVLSDRAPFAAPSPFAELVLPP KQ*

Gene Symbol:	TYMP
Accession:	NM_001113756
Location:	EXON
Amino Acid Prediction:	Q to K (nonsynonymous)
Amino Acid Position:	481

Amino Acid Sequence (Calculated using NCBI transcript definition)
MAALMTPGTGAPPAPGDFSGEGSQGLPDPSPEPKQLPELIRMKRDGGRLSEADIRGFVAAVVNGSAQGAQIGAMLMAIRL RGMDLEETSVLTQALAQSGQQLEWPEAWRQQLVDKHSTGGVGDKVSLVLAPALAACGCKVPMISGRGLGHTGGTLDKLES IPGFNVIQSPEQMQVLLDQAGCCIVGQSEQLVPADGILYAARDVTATVDSLPLITASILSKKLVEGLSALVVDVKFGGAA VFPNQEQARELAKTLVGVGASLGLRVAAALTAMDKPLGRCVGHALEVEEALLCMDGAGPPDLRDLVTTLGGALLWLSGHA GTQAQGAARVAAALDDGSALGRFERMLAAQGVDPGLARALCSGSPAERRQLLPRAREQEELLAPADGTVELVRALPLALV LHELGAGRSRAGEPLRLGVGAELLVDVGQRLRRGTPWLRVHRDGPALSGPQSRALQEALVLSDRAPFAAPSPFAELVLPP KQ*

Gene Symbol:	TYMP
Accession:	NM_001257989
Location:	EXON
Amino Acid Prediction:	Q to K (nonsynonymous)
Amino Acid Position:	486

Amino Acid Sequence (Calculated using NCBI transcript definition)
MAALMTPGTGAPPAPGDFSGEGSQGLPDPSPEPKQLPELIRMKRDGGRLSEADIRGFVAAVVNGSAQGAQIGAMLMAIRL RGMDLEETSVLTQALAQSGQQLEWPEAWRQQLVDKHSTGGVGDKVSLVLAPALAACGCKVPMISGRGLGHTGGTLDKLES IPGFNVIQSPEQMQVLLDQAGCCIVGQSEQLVPADGILYAARDVTATVDSLPLITASILSKKLVEGLSALVVDVKFGGAA VFPNQEQARELAKTLVGVGASLGLRVAAALTAMDKPLGRCVGHALEVEEALLCMDGAGPPDLRDLVTTLGGALLWLSGHA GTQAQGAARVAAALDDGSALGRFERMLAAQGVDPGLARALCSGSPAERRQLLPRAREQEELLAPADAPLPAGTVELVRAL PLALVLHELGAGRSRAGEPLRLGVGAELLVDVGQRLRRGTPWLRVHRDGPALSGPQSRALQEALVLSDRAPFAAPSPFAE LVLPPKQ*

Gene Symbol:	TYMP
Accession:	NM_001113755
Location:	EXON
Amino Acid Prediction:	Q to K (nonsynonymous)
Amino Acid Position:	481

Amino Acid Sequence (Calculated using NCBI transcript definition)
MAALMTPGTGAPPAPGDFSGEGSQGLPDPSPEPKQLPELIRMKRDGGRLSEADIRGFVAAVVNGSAQGAQIGAMLMAIRL RGMDLEETSVLTQALAQSGQQLEWPEAWRQQLVDKHSTGGVGDKVSLVLAPALAACGCKVPMISGRGLGHTGGTLDKLES IPGFNVIQSPEQMQVLLDQAGCCIVGQSEQLVPADGILYAARDVTATVDSLPLITASILSKKLVEGLSALVVDVKFGGAA VFPNQEQARELAKTLVGVGASLGLRVAAALTAMDKPLGRCVGHALEVEEALLCMDGAGPPDLRDLVTTLGGALLWLSGHA GTQAQGAARVAAALDDGSALGRFERMLAAQGVDPGLARALCSGSPAERRQLLPRAREQEELLAPADGTVELVRALPLALV LHELGAGRSRAGEPLRLGVGAELLVDVGQRLRRGTPWLRVHRDGPALSGPQSRALQEALVLSDRAPFAAPSPFAELVLPP KQ*

Gene Symbol:	TYMP
Accession:	NM_001953
Location:	EXON
Amino Acid Prediction:	Q to K (nonsynonymous)
Amino Acid Position:	481

Amino Acid Sequence (Calculated using NCBI transcript definition)
MAALMTPGTGAPPAPGDFSGEGSQGLPDPSPEPKQLPELIRMKRDGGRLSEADIRGFVAAVVNGSAQGAQIGAMLMAIRL RGMDLEETSVLTQALAQSGQQLEWPEAWRQQLVDKHSTGGVGDKVSLVLAPALAACGCKVPMISGRGLGHTGGTLDKLES IPGFNVIQSPEQMQVLLDQAGCCIVGQSEQLVPADGILYAARDVTATVDSLPLITASILSKKLVEGLSALVVDVKFGGAA VFPNQEQARELAKTLVGVGASLGLRVAAALTAMDKPLGRCVGHALEVEEALLCMDGAGPPDLRDLVTTLGGALLWLSGHA GTQAQGAARVAAALDDGSALGRFERMLAAQGVDPGLARALCSGSPAERRQLLPRAREQEELLAPADGTVELVRALPLALV LHELGAGRSRAGEPLRLGVGAELLVDVGQRLRRGTPWLRVHRDGPALSGPQSRALQEALVLSDRAPFAAPSPFAELVLPP KQ*

Gene Symbol:	SCO2
Accession:	NM_005138
Location:	INTRON

Gene Symbol:	SCO2
Accession:	NM_001169111
Location:	INTRON

Variant Samples

ClinVar GRCh37

ClinVar GRCh38

Additional References at PubMed

PMID:25741868	PMID:28492532

Additional Information

External Database Links

Database	Acc Id	Source(s)
ClinVar	RCV000668426	CLINVAR
	RCV002531198	CLINVAR
	RCV003488791	CLINVAR
	RCV003892517	CLINVAR
dbSNP (RS)	rs200735968	CLINVAR
MedGen	C3661900	CLINVAR
	C4551995	CLINVAR
	CN169374	CLINVAR
NCBI Gene	SCO2	CLINVAR
	TYMP	CLINVAR
OMIM	131222	CLINVAR
	603041	CLINVAR
	604272	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)

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Variant: RGD:13792209 - Homo sapiens

Imported Disease Annotations - ClinVar