View genomic variant #0000025751

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

1 entry on 1 page. Showing entry 1.

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
LRPPRC	00000168	NM_133259.3	0000025751	./.	-	-	c.79_80insCGCTCTCCCTGCGCCTCC	p.(Pro21_Leu26dup)	-	-	-	-

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	RCV001396939;
Chromosome	2:44223006..44223006
ClinVar Allele ID	1069640
Disease database name and identifier	MedGen:C3661900
ClinVar preferred disease name	not provided
HGVS variant names	NC 000002.11:g.44223006G>C
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.	LRPPRC:10128
Molecular consequence	SO:0001819|synonymous variant
Allele origin	germline
dbSNP ID	1266747593
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000665919;
Chromosome	2:44223007..44223008
ClinVar Allele ID	542132
Disease database name and identifier	MONDO:MONDO:0009069, MedGen:C1857355, OMIM:220111, Orphanet:70472
ClinVar preferred disease name	Congenital lactic acidosis, Saguenay-Lac-Saint-Jean type
HGVS variant names	NC 000002.11:g.44223016 44223033dup
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.	LRPPRC:10128
Molecular consequence	SO:0001821|inframe insertion
Allele origin	unknown
dbSNP ID	760874906
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000199980; RCV000322781; RCV000757440;
Chromosome	2:44223008..44223008
Allele frequencies from ESP	0.00404
Allele frequencies from TGP	0.00978
ClinVar Allele ID	210866
Disease database name and identifier	MONDO:MONDO:0009069, MedGen:C1857355, OMIM:220111, Orphanet:70472|MedGen:CN169374|MedGen:C3661900
ClinVar preferred disease name	Congenital lactic acidosis, Saguenay-Lac-Saint-Jean type|not specified|not provided
HGVS variant names	NC 000002.11:g.44223008G>A
ClinVar review status	criteria provided, conflicting interpretations
Clinical Significance	Conflicting interpretations of pathogenicity
Conflicting clinical significance	Uncertain significance(1)|Benign(3)
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Variant clinical sources reported	ClinGen:CA324529
Gene symbol:Gene id.	LRPPRC:10128
Molecular consequence	SO:0001583|missense variant
Allele origin	germline
dbSNP ID	116727742
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV003441358;
Chromosome	2:44223008..44223008
ClinVar Allele ID	2830143
Disease database name and identifier	MedGen:C3661900
ClinVar preferred disease name	not provided
HGVS variant names	NC 000002.11:g.44223008G>C
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.	LRPPRC:10128
Molecular consequence	SO:0001583|missense variant
Allele origin	germline
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