RGD:15134960 Rat Genome Database

Variant: RGD:15134960 - Homo sapiens

RGD ID:

15134960

RS ID:

rs1013301590

ClinVar ID:

CV773628

Genic Status:

GENIC

Type:

SNV (SO:0001483)

Associated Genes:

LOC130067862 SCO2 TYMP

Reference Nucleotide:

Variant Nucleotide:

Position

Assembly	Chr	Position
GRCh37	22	50,964,488
GRCh38	22	50,526,059

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_001169110.1:c.-72G>A NM_001113755.3:c.1242G>A NM_001113756.3:c.1242G>A NM_001257988.1:c.1242G>A More...	11/17/2020	5 prime utr variant	likely benign	Mitochondrial neurogastrointestinal encephalopathy syndrome; MNGIE syndrome; Myoneurogastrointestinal encephalopathy syndrome; none provided; Thymidine phosphorylase deficiency

Disease Annotations Click to see Annotation Detail View

mitochondrial DNA depletion syndrome 8A (IAGP)

Mitochondrial DNA Depletion Syndrome, MNGIE Type (IAGP)

Variant Details

Variant Transcripts

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

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

Gene Symbol:	TYMP
Accession:	NM_001113756
Location:	EXON
Amino Acid Prediction:	P to P (synonymous)
Amino Acid Position:	414

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

Gene Symbol:	TYMP
Accession:	NM_001257988
Location:	EXON
Amino Acid Prediction:	P to P (synonymous)
Amino Acid Position:	414

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

Gene Symbol:	TYMP
Accession:	NM_001113755
Location:	EXON
Amino Acid Prediction:	P to P (synonymous)
Amino Acid Position:	414

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

Gene Symbol:	TYMP
Accession:	NM_001953
Location:	EXON
Amino Acid Prediction:	P to P (synonymous)
Amino Acid Position:	414

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

Gene Symbol:	TYMP
Accession:	NM_001257989
Location:	EXON
Amino Acid Prediction:	P to P (synonymous)
Amino Acid Position:	419

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

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:28492532

Additional Information

External Database Links

Database	Acc Id	Source(s)
ClinVar	RCV000942836	CLINVAR
	RCV001272323	CLINVAR
dbSNP (RS)	rs1013301590	CLINVAR
MedGen	C0872218	CLINVAR
	C3661900	CLINVAR
NCBI Gene	LOC130067862	CLINVAR
	SCO2	CLINVAR
	TYMP	CLINVAR
OMIM	131222	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:15134960 - Homo sapiens

Imported Disease Annotations - ClinVar