View genomic variant #0000002545

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.89876722G>C
Published as	-
GERP	3.940
Segregation	-
DB-ID	POLG_000052 See all 2 reported entries
MSCV	MSCV_0002545
dbSNP ID	-
Frequency	-
Sources	; POLG_MUT_DB;
Reference	-
Variant remarks	-
Genetic origin	-
Variant_disease	-
Average frequency (large NGS studies)	Variant not found in online data sets
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.

Legend

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	0000002545	+?/+?	-	2/23	c.264C>G	p.(Phe88Leu)	benign(0.071)	missense_variant	-	deleterious(0.03)
POLG	00000267	NM_002693.2	0000002545	+?/+?	-	2/23	c.264C>G	p.(Phe88Leu)	benign(0.071)	missense_variant	-	deleterious(0.03)

Legend

ClinVar @ MSeqDR
RCVaccession	RCV000118014; RCV000227341; RCV000436920; RCV001116623; RCV001847711; RCV002313915;
Chromosome	15:89876722..89876722
Allele frequencies from ESP	0.00177
Allele frequencies from TGP	0.00080
ClinVar Allele ID	135438
Disease database name and identifier	MedGen:C4763519\|MeSH:D030342, MedGen:C0950123\|MedGen:CN169374\|MedGen:C3661900\|MONDO:MONDO:0019064, MedGen:C0037773, OMIM:PS303350, Orphanet:685\|MONDO:MONDO:0008758, MedGen:C0205710, OMIM:203700, Orphanet:726
ClinVar preferred disease name	POLG-Related Spectrum Disorders\|Inborn genetic diseases\|not specified\|not provided\|Hereditary spastic paraplegia\|Progressive sclerosing poliodystrophy
HGVS variant names	NC 000015.9:g.89876722G>A
ClinVar review status	criteria provided, conflicting interpretations
Clinical Significance	Conflicting interpretations of pathogenicity
Conflicting clinical significance	Uncertain significance(1)\|Benign(5)\|Likely benign(8)
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Variant clinical sources reported	ClinGen:CA288984
Gene symbol:Gene id.	POLG:5428\|POLGARF:125316803
Molecular consequence	SO:0001819\|synonymous variant
Allele origin	germline
dbSNP ID	144439703
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV000431950; RCV000693072;
Chromosome 15:89876722..89876722
ClinVar Allele ID 376833
Disease database name and identifier MONDO:MONDO:0008758, MedGen:C0205710, OMIM:203700, Orphanet:726|MedGen:C3661900
ClinVar preferred disease name Progressive sclerosing poliodystrophy|not provided
HGVS variant names NC 000015.9:g.89876722G>C
ClinVar review status criteria provided, conflicting interpretations
Clinical Significance Conflicting interpretations of pathogenicity
Conflicting clinical significance Pathogenic(1)|Likely pathogenic(1)|Uncertain significance(2)
Variant type single nucleotide variant
Sequence Ontology for variant type SO:0001483
Variant clinical sources reported ClinGen:CA7725145
Gene symbol:Gene id. POLG:5428|POLGARF:125316803
Molecular consequence SO:0001583|missense variant
Allele origin germline
dbSNP ID 144439703
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