View genomic variant #0000026356

Variant on transcripts

Legend

Please note that a short description of a certain column can be displayed when you move your mouse cursor over the column's header and hold it still. Below, a more detailed description is shown per column.

Affects function: The variant's effect on the protein's function, in the format 'R/C' where R is the value reported by the source and C is the value concluded by the curator; '+' indicating the variant affects function, '+?' probably affects function, '+*' affects function, not associated with individual's disease phenotype, '#' affects function, not associated with any known disease phenotype, '-' does not affect function, '-?' probably does not affect function, '?' effect unknown, '.' effect not classified.

Location: Location of variant at DNA level; note that the variant location can also be derived from the variant description.
All options:

• 5' gene flanking
• 5' UTR
• Exon
• Intron
• 3' UTR
• 3' gene flanking

Exon: Number of exon/intron containing variant; 2 = exon 2, 12i = intron 12, 2i_7i = exons 3 to 7, 8i_9 = border intron 8/exon 9.

DNA change (cDNA): Description of variant at DNA level, based on a coding DNA reference sequence (following HGVS recommendations); e.g. c.123C>T, c.123_145del, c.123_126dup.

Protein: Description of variant at protein level (following HGVS recommendations).

• p.(Arg345Pro) = change predicted from DNA (RNA not analysed)
• p.Arg345Pro = change derived from RNA analysis
• p.? = unknown effect
• p.0? = probably no protein produced

PolyPhen: Effect of variant, predicted by PolyPhen.
All options:

• benign = Benign
• possiblyDamaging = Possibly damaging
• probablyDamaging = Probably damaging
• noPrediction = No prediction

GVS function: The functional annotation of this position from the Genome Variation Server.
All options:

• intergenic
• near-gene-5
• utr-5
• coding
• coding-near-splice
• coding-synonymous
• coding-synonymous-near-splice
• codingComplex
• codingComplex-near-splice
• frameshift
• frameshift-near-splice
• missense
• missense-near-splice
• splice-5
• intron
• splice-3
• stop-gained
• stop-gained-near-splice
• stop-lost
• stop-lost-near-splice
• utr-3
• near-gene-3

Splice distance: The distance to the nearest splice site.

SIFT: SIFT Annotation

3 entries on 1 page. Showing entries 1 - 3.

10 per page 25 per page 50 per page 100 per page 250 per page 500 per page 1000 per page

Legend

Gene	Transcript ID	Transcript	Variant ID	Affects function	Location	Exon	DNA change (cDNA)	Protein	PolyPhen	GVS function	Splice distance	SIFT
SLC22A5	00001145	NM_003060.3	0000026356	./.	-	-	c.134del	p.(Pro46Argfs*13)	-	-	-	-
SLC22A5	00001144	XM_005272055.1	0000026356	./.	-	-	c.134del	-	-	-	-	-
SLC22A5	00001146	XM_005272056.1	0000026356	./.	-	-	c.-267del	p.(=)	-	-	-	-

10 per page 25 per page 50 per page 100 per page 250 per page 500 per page 1000 per page

Legend

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000635352; RCV002226476;
Chromosome	5:131705797..131705797
Allele frequencies from ESP	0.00008
Allele frequencies from ExAC	0.00003
ClinVar Allele ID	521014
Disease database name and identifier	MONDO:MONDO:0008919, MedGen:C0342788, OMIM:212140, Orphanet:158|Human Phenotype Ontology:HP:0003234, MedGen:C1142132
ClinVar preferred disease name	Renal carnitine transport defect|Decreased circulating carnitine concentration
HGVS variant names	NC 000005.9:g.131705797A>G
ClinVar review status	criteria provided, single submitter
Clinical Significance	Uncertain significance
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Variant clinical sources reported	ClinGen:CA3403795
Gene symbol:Gene id.	SLC22A5:6584
Molecular consequence	SO:0001583|missense variant
Allele origin	germline
dbSNP ID	376438682
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000673009;
Chromosome	5:131705798..131705798
ClinVar Allele ID	543679
Disease database name and identifier	MONDO:MONDO:0008919, MedGen:C0342788, OMIM:212140, Orphanet:158
ClinVar preferred disease name	Renal carnitine transport defect
HGVS variant names	NC 000005.9:g.131705801del
ClinVar review status	criteria provided, single submitter
Clinical Significance	Likely pathogenic
Variant type	Deletion
Sequence Ontology for variant type	SO:0000159
Gene symbol:Gene id.	SLC22A5:6584
Molecular consequence	SO:0001589|frameshift variant
Allele origin	unknown
dbSNP ID	762986044
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV002306118; RCV003102287;
Chromosome	5:131705798..131705798
ClinVar Allele ID	1780513
Disease database name and identifier	MONDO:MONDO:0008919, MedGen:C0342788, OMIM:212140, Orphanet:158|MedGen:CN517202
ClinVar preferred disease name	Renal carnitine transport defect|not provided
HGVS variant names	NC 000005.9:g.131705798C>A
ClinVar review status	criteria provided, multiple submitters, no conflicts
Clinical Significance	Uncertain significance
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Gene symbol:Gene id.	SLC22A5:6584
Molecular consequence	SO:0001583|missense variant
Allele origin	germline
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV001500656;
Chromosome	5:131705799..131705799
ClinVar Allele ID	782130
Disease database name and identifier	MONDO:MONDO:0008919, MedGen:C0342788, OMIM:212140, Orphanet:158
ClinVar preferred disease name	Renal carnitine transport defect
HGVS variant names	NC 000005.9:g.131705799C>A
ClinVar review status	criteria provided, single submitter
Clinical Significance	Likely benign
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Gene symbol:Gene id.	SLC22A5:6584
Molecular consequence	SO:0001819|synonymous variant
Allele origin	germline
dbSNP ID	202000855
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV002181411;
Chromosome	5:131705799..131705799
ClinVar Allele ID	1575519
Disease database name and identifier	MONDO:MONDO:0008919, MedGen:C0342788, OMIM:212140, Orphanet:158
ClinVar preferred disease name	Renal carnitine transport defect
HGVS variant names	NC 000005.9:g.131705799C>G
ClinVar review status	criteria provided, single submitter
Clinical Significance	Likely benign
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Gene symbol:Gene id.	SLC22A5:6584
Molecular consequence	SO:0001819|synonymous variant
Allele origin	germline
dbSNP ID	202000855
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV001415413;
Chromosome	5:131705799..131705799
Allele frequencies from TGP	0.00020
ClinVar Allele ID	1072190
Disease database name and identifier	MONDO:MONDO:0008919, MedGen:C0342788, OMIM:212140, Orphanet:158
ClinVar preferred disease name	Renal carnitine transport defect
HGVS variant names	NC 000005.9:g.131705799C>T
ClinVar review status	criteria provided, single submitter
Clinical Significance	Likely benign
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Gene symbol:Gene id.	SLC22A5:6584
Molecular consequence	SO:0001819|synonymous variant
Allele origin	germline
dbSNP ID	202000855
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

MSeqDR View Variant at Gbrowse

Mitomap Mitochondrial Variant Phenotype Information:

None

Ensembl Variant Phenotype Information:

None