View genomic variant #0000000609

Chromosome	15
Allele	Unknown
Affects function (as reported)	Does not affect function
Affects function (by curator)	Does not affect function
Type	subst
DNA change (genomic) (Relative to hg19 / GRCh37)	g.89876408C>T
Published as	-
GERP	2.650
Segregation	-
DB-ID	POLG_000018 See all 2 reported entries
MSCV	MSCV_0000609
dbSNP ID	rs3176162
Frequency	-
Sources	; clinVar; ensembl; POLG_MUT_DB;
Reference	20301791
Variant remarks	-
Genetic origin	-
Variant_disease	-
Average frequency (large NGS studies)	0.00054 View details
Owner	LOVD

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

2 entries on 1 page. Showing entries 1 - 2.

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Gene	Transcript ID	Transcript	Variant ID	Affects function	Location	Exon	DNA change (cDNA)	Protein	PolyPhen	GVS function	Splice distance	SIFT
POLG	00000266	NM_001126131.1	0000000609	-/-	-	2/23	c.578G>A	p.(Arg193Gln)	benign(0.006)	missense_variant	-	tolerated(0.47)
POLG	00000267	NM_002693.2	0000000609	-/-	-	2/23	c.578G>A	p.(Arg193Gln)	benign(0.006)	missense_variant	-	tolerated(0.47)

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ClinVar @ MSeqDR
RCVaccession	RCV002736453;
Chromosome	15:89876408..89876408
ClinVar Allele ID	2027204
Disease database name and identifier	MONDO:MONDO:0008758, MedGen:C0205710, OMIM:203700, Orphanet:726
ClinVar preferred disease name	Progressive sclerosing poliodystrophy
HGVS variant names	NC 000015.9:g.89876408C>G
ClinVar review status	criteria provided, single submitter
Clinical Significance	Uncertain significance
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Gene symbol:Gene id.	POLG:5428\|POLGARF:125316803
Molecular consequence	SO:0001583\|missense variant, SO:0001819\|synonymous variant
Allele origin	germline
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV000020482; RCV000541557; RCV000724388; RCV001121514; RCV002313715; RCV002476997;
Chromosome 15:89876408..89876408
Allele frequencies from ESP 0.00054
Allele frequencies from ExAC 0.00023
Allele frequencies from TGP 0.00060
ClinVar Allele ID 34170
Disease database name and identifier MedGen:C4763519|MeSH:D030342, MedGen:C0950123|MONDO:MONDO:0011283, MedGen:C4551995, OMIM:603041, Orphanet:298|MONDO:MONDO:0008758, MedGen:C0205710, OMIM:203700, Orphanet:726|MONDO:MONDO:0009783, MedGen:C4225153, OMIM:258450, Orphanet:254886|MONDO:MONDO:0013350, MedGen:C3150914, OMIM:613662, Orphanet:298|MONDO:MONDO:0011835, MedGen:C1843851, OMIM:607459, Orphanet:70595|MONDO:MONDO:0024528, MedGen:C1834846, OMIM:157640|MONDO:MONDO:0044970, MeSH:D028361, MedGen:C0751651, Orphanet:68380|MedGen:C3661900
ClinVar preferred disease name POLG-Related Spectrum Disorders|Inborn genetic diseases|Mitochondrial DNA depletion syndrome 1|Progressive sclerosing poliodystrophy|Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1|Mitochondrial DNA depletion syndrome 4b|Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis|Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 1|Mitochondrial disease|not provided
HGVS variant names NC 000015.9:g.89876408C>T
ClinVar review status reviewed by expert panel
Clinical Significance Uncertain significance
Variant type single nucleotide variant
Sequence Ontology for variant type SO:0001483
Variant clinical sources reported ClinGen:CA241475|UniProtKB:P54098#VAR 019267
Gene symbol:Gene id. POLG:5428|POLGARF:125316803
Molecular consequence SO:0001583|missense variant
Allele origin germline
dbSNP ID 3176162
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