View genomic variant #0000000860

Chromosome	2
Allele	Unknown
Affects function (as reported)	Affects function
Affects function (by curator)	Affects function
Type	subst
DNA change (genomic) (Relative to hg19 / GRCh37)	g.211504769G>A
Published as	-
GERP	5.420
Segregation	-
DB-ID	CPS1_000004 See all 2 reported entries
MSCV	MSCV_0000860
dbSNP ID	rs121912595
Frequency	-
Sources	; clinVar; Ensembl;
Reference	17310273
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

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

Legend

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	0000000860	+/+	-	25/39	c.2963G>A	p.?	probably_damaging(1)	missense_variant	-	deleterious(0)
CPS1	00000659	NM_001122634.2	0000000860	+/+	-	14/28	c.1592G>A	p.(Gly531Asp)	probably_damaging(1)	missense_variant	-	deleterious(0)
CPS1	00000658	NM_001875.4	0000000860	+/+	-	24/38	c.2945G>A	p.(Gly982Asp)	probably_damaging(1)	missense_variant	-	deleterious(0)

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ClinVar @ MSeqDR
RCVaccession	RCV000002526;
Chromosome	2:211504769..211504769
ClinVar Allele ID	17463
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.211504769G>A
ClinVar review status	criteria provided, single submitter
Clinical Significance	Likely pathogenic
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Variant clinical sources reported	ClinGen:CA115537\|OMIM:608307.0007\|UniProtKB:P31327#VAR 063570
Gene symbol:Gene id.	CPS1:1373
Molecular consequence	SO:0001583\|missense variant, SO:0001619\|non-coding transcript variant
Allele origin	germline
dbSNP ID	121912595
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV000668782; RCV002531211;
Chromosome 2:211504769..211504769
Allele frequencies from ExAC 0.00001
ClinVar Allele ID 541822
Disease database name and identifier MeSH:D030342, MedGen:C0950123|MONDO:MONDO:0009376, MedGen:C4082171, OMIM:237300, Orphanet:147
ClinVar preferred disease name Inborn genetic diseases|Congenital hyperammonemia, type I
HGVS variant names NC 000002.11:g.211504769G>T
ClinVar review status criteria provided, multiple submitters, no conflicts
Clinical Significance Uncertain significance
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 121912595
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