View genomic variant #0000019533

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

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

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Gene	Transcript ID	Transcript	Variant ID	Affects function	Location	Exon	DNA change (cDNA)	Protein	PolyPhen	GVS function	Splice distance	SIFT
CPS1	00000657	NM_001122633.2	0000019533	./.	-	-	c.2425C>T	p.(Arg809Cys)	-	-	-	-
CPS1	00000659	NM_001122634.2	0000019533	./.	-	-	c.1054C>T	p.(Arg352Cys)	-	-	-	-
CPS1	00000658	NM_001875.4	0000019533	./.	-	-	c.2407C>T	p.(Arg803Cys)	-	-	-	-

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ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV001974483;
Chromosome	2:211476856..211476857
ClinVar Allele ID	1500665
Disease database name and identifier	MONDO:MONDO:0009376, MedGen:C4082171, OMIM:237300, Orphanet:147
ClinVar preferred disease name	Congenital hyperammonemia, type I
HGVS variant names	NC 000002.11:g.211476857dup
ClinVar review status	criteria provided, single submitter
Clinical Significance	Pathogenic
Variant type	Duplication
Sequence Ontology for variant type	SO:1000035
Gene symbol:Gene id.	CPS1:1373
Molecular consequence	SO:0001589|frameshift variant, SO:0001619|non-coding transcript variant
Allele origin	germline
dbSNP ID	2105859007
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000813104; RCV002495136; RCV003467464;
Chromosome	2:211476856..211476856
ClinVar Allele ID	629357
Disease database name and identifier	MONDO:MONDO:0009376, MedGen:C4082171, OMIM:237300, Orphanet:147|MONDO:MONDO:0014151, MedGen:C3714958, OMIM:615371
ClinVar preferred disease name	Congenital hyperammonemia, type I|Pulmonary hypertension, neonatal, susceptibility to
HGVS variant names	NC 000002.11:g.211476856C>G
ClinVar review status	criteria provided, multiple submitters, no conflicts
Clinical Significance	Pathogenic/Likely pathogenic
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Gene symbol:Gene id.	CPS1:1373
Molecular consequence	SO:0001583|missense variant, SO:0001619|non-coding transcript variant
Allele origin	germline
dbSNP ID	201716417
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000552829; RCV002298663;
Chromosome	2:211476856..211476856
ClinVar Allele ID	450459
Disease database name and identifier	MedGen:CN169374|MONDO:MONDO:0009376, MedGen:C4082171, OMIM:237300, Orphanet:147
ClinVar preferred disease name	not specified|Congenital hyperammonemia, type I
HGVS variant names	NC 000002.11:g.211476856C>T
ClinVar review status	criteria provided, conflicting interpretations
Clinical Significance	Conflicting interpretations of pathogenicity
Conflicting clinical significance	Pathogenic(1)|Uncertain significance(2)
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Variant clinical sources reported	ClinGen:CA2086634
Gene symbol:Gene id.	CPS1:1373
Molecular consequence	SO:0001583|missense variant, SO:0001619|non-coding transcript variant
Allele origin	germline
dbSNP ID	201716417
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