View genomic variant #0000017754

Variant on transcripts

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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	0000017754	./.	-	-	c.158_166del	p.(Gln53_Gln55del)	-	-	-	-
POLG	00000267	NM_002693.2	0000017754	./.	-	-	c.158_166del	p.(Gln53_Gln55del)	-	-	-	-

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ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000530802;
Chromosome	15:89876819..89876819
ClinVar Allele ID	464607
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.89876819G>C
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:CA393773955
Gene symbol:Gene id.	POLG:5428|POLGARF:125316803
Molecular consequence	SO:0001583|missense variant
Allele origin	germline
dbSNP ID	1022612492
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV003108957;
Chromosome	15:89876819..89876820
ClinVar Allele ID	1943863
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.89876821CTG[3]
ClinVar review status	criteria provided, single submitter
Clinical Significance	Uncertain significance
Variant type	Microsatellite
Sequence Ontology for variant type	SO:0000289
Gene symbol:Gene id.	POLG:5428|POLGARF:125316803
Molecular consequence	SO:0001820|inframe indel, SO:0001821|inframe insertion
Allele origin	germline
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV002847224;
Chromosome	15:89876819..89876820
ClinVar Allele ID	2083467
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.89876821CTG[4]
ClinVar review status	criteria provided, single submitter
Clinical Significance	Uncertain significance
Variant type	Microsatellite
Sequence Ontology for variant type	SO:0000289
Gene symbol:Gene id.	POLG:5428|POLGARF:125316803
Molecular consequence	SO:0001820|inframe indel, SO:0001821|inframe insertion
Allele origin	germline
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000633556; RCV001572551;
Chromosome	15:89876819..89876820
ClinVar Allele ID	529124
Disease database name and identifier	MONDO:MONDO:0008758, MedGen:C0205710, OMIM:203700, Orphanet:726|MedGen:CN517202
ClinVar preferred disease name	Progressive sclerosing poliodystrophy|not provided
HGVS variant names	NC 000015.9:g.89876827 89876835dup
ClinVar review status	criteria provided, multiple submitters, no conflicts
Clinical Significance	Likely benign
Variant type	Duplication
Sequence Ontology for variant type	SO:1000035
Variant clinical sources reported	ClinGen:CA7725174
Gene symbol:Gene id.	POLG:5428|POLGARF:125316803
Molecular consequence	SO:0001821|inframe insertion
Allele origin	germline
dbSNP ID	769735492
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV001350359;
Chromosome	15:89876819..89876820
ClinVar Allele ID	1032203
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.89876827 89876844dup
ClinVar review status	criteria provided, single submitter
Clinical Significance	Uncertain significance
Variant type	Duplication
Sequence Ontology for variant type	SO:1000035
Gene symbol:Gene id.	POLG:5428|POLGARF:125316803
Molecular consequence	SO:0001821|inframe insertion
Allele origin	germline
dbSNP ID	773536141
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV002996880;
Chromosome	15:89876819..89876820
ClinVar Allele ID	2152955
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.89876827 89876847dup
ClinVar review status	criteria provided, single submitter
Clinical Significance	Uncertain significance
Variant type	Duplication
Sequence Ontology for variant type	SO:1000035
Gene symbol:Gene id.	POLG:5428|POLGARF:125316803
Molecular consequence	SO:0001820|inframe indel, SO:0001821|inframe insertion
Allele origin	germline
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000633560;
Chromosome	15:89876819..89876820
ClinVar Allele ID	529127
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.89876827 89876850dup
ClinVar review status	criteria provided, single submitter
Clinical Significance	Likely benign
Variant type	Duplication
Sequence Ontology for variant type	SO:1000035
Variant clinical sources reported	ClinGen:CA7725172
Gene symbol:Gene id.	POLG:5428|POLGARF:125316803
Molecular consequence	SO:0001821|inframe insertion
Allele origin	germline
dbSNP ID	1555454325
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000597328; RCV000633570; RCV001081529; RCV002404611;
Chromosome	15:89876820..89876828
ClinVar Allele ID	492779
Disease database name and identifier	MONDO:MONDO:0008758, MedGen:C0205710, OMIM:203700, Orphanet:726|MeSH:D030342, MedGen:C0950123|MedGen:CN169374|MedGen:CN517202
ClinVar preferred disease name	Progressive sclerosing poliodystrophy|Inborn genetic diseases|not specified|not provided
HGVS variant names	NC 000015.9:g.89876827 89876835del
ClinVar review status	criteria provided, conflicting interpretations
Clinical Significance	Conflicting interpretations of pathogenicity
Conflicting clinical significance	Uncertain significance(1)|Benign(1)|Likely benign(3)
Variant type	Deletion
Sequence Ontology for variant type	SO:0000159
Variant clinical sources reported	ClinGen:CA7725171
Gene symbol:Gene id.	POLG:5428|POLGARF:125316803
Molecular consequence	SO:0001822|inframe deletion
Allele origin	germline
dbSNP ID	769735492
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000188536; RCV000726981; RCV002054220;
Chromosome	15:89876820..89876831
ClinVar Allele ID	203053
Disease database name and identifier	MedGen:CN517202|MedGen:CN169374|MONDO:MONDO:0008758, MedGen:C0205710, OMIM:203700, Orphanet:726
ClinVar preferred disease name	not provided|not specified|Progressive sclerosing poliodystrophy
HGVS variant names	NC 000015.9:g.89876827 89876838del
ClinVar review status	criteria provided, conflicting interpretations
Clinical Significance	Conflicting interpretations of pathogenicity
Conflicting clinical significance	Uncertain significance(1)|Likely benign(2)
Variant type	Deletion
Sequence Ontology for variant type	SO:0000159
Variant clinical sources reported	ClinGen:CA316625
Gene symbol:Gene id.	POLG:5428|POLGARF:125316803
Molecular consequence	SO:0001822|inframe deletion
Allele origin	germline
dbSNP ID	761909257
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV003047433;
Chromosome	15:89876820..89876843
ClinVar Allele ID	2178039
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.89876827 89876850del
ClinVar review status	criteria provided, single submitter
Clinical Significance	Uncertain significance
Variant type	Deletion
Sequence Ontology for variant type	SO:0000159
Gene symbol:Gene id.	POLG:5428|POLGARF:125316803
Molecular consequence	SO:0001820|inframe indel, SO:0001822|inframe deletion
Allele origin	germline
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000870468; RCV001722389;
Chromosome	15:89876821..89876822
ClinVar Allele ID	409383
Disease database name and identifier	MedGen:C3661900|MONDO:MONDO:0008758, MedGen:C0205710, OMIM:203700, Orphanet:726
ClinVar preferred disease name	not provided|Progressive sclerosing poliodystrophy
HGVS variant names	NC 000015.9:g.89876827 89876832dup
ClinVar review status	criteria provided, conflicting interpretations
Clinical Significance	Conflicting interpretations of pathogenicity
Conflicting clinical significance	Uncertain significance(1)|Likely benign(2)
Variant type	Duplication
Sequence Ontology for variant type	SO:1000035
Variant clinical sources reported	ClinGen:CA7725176
Gene symbol:Gene id.	POLG:5428|POLGARF:125316803
Molecular consequence	SO:0001821|inframe insertion
Allele origin	germline
dbSNP ID	760135553
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV001567293;
Chromosome	15:89876821..89876821
ClinVar Allele ID	1191733
Disease database name and identifier	MedGen:C3661900
ClinVar preferred disease name	not provided
HGVS variant names	NC 000015.9:g.89876821C>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.	POLG:5428|POLGARF:125316803
Molecular consequence	SO:0001819|synonymous variant
Allele origin	germline
dbSNP ID	2141815770
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000758286;
Chromosome	15:89876828..89876828
Allele frequencies from ExAC	0.00010
Allele frequencies from TGP	0.00040
ClinVar Allele ID	610803
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.89876828T>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
Allele origin	germline
dbSNP ID	527965158
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