View genomic variant #0000000994

Chromosome	4
Allele	Unknown
Affects function (as reported)	Affects function
Affects function (by curator)	Affects function
Type	subst
DNA change (genomic) (Relative to hg19 / GRCh37)	g.17510986A>G
Published as	-
GERP	5.520
Segregation	-
DB-ID	QDPR_000003
MSCV	MSCV_0000994
dbSNP ID	rs104893865
Frequency	-
Sources	;
Reference	9341885
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

1 entry on 1 page. Showing entry 1.

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Gene	Transcript ID	Transcript	Variant ID	Affects function	Location	Exon	DNA change (cDNA)	Protein	PolyPhen	GVS function	Splice distance	SIFT
QDPR	00002711	NM_000320.2	0000000994	?/?	-	2/7	c.106T>C	p.(Trp36Arg)	probably_damaging(0.995)	missense_variant,splice_region_variant	-	tolerated(0.24)

Legend

ClinVar @ MSeqDR
RCVaccession	RCV003233063;
Chromosome	4:17510986..17510986
ClinVar Allele ID	2669614
Disease database name and identifier	MONDO:MONDO:0009862, MedGen:C0268465, OMIM:261630, Orphanet:226, Orphanet:238583
ClinVar preferred disease name	Dihydropteridine reductase deficiency
HGVS variant names	NC 000004.11:g.17510986A>C
ClinVar review status	criteria provided, single submitter
Clinical Significance	Likely pathogenic
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Gene symbol:Gene id.	QDPR:5860
Molecular consequence	SO:0001583\|missense variant, SO:0001619\|non-coding transcript variant, SO:0001627\|intron variant
Allele origin	unknown
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV000000521;
Chromosome 4:17510986..17510986
ClinVar Allele ID 15531
Disease database name and identifier MONDO:MONDO:0009862, MedGen:C0268465, OMIM:261630, Orphanet:226, Orphanet:238583
ClinVar preferred disease name Dihydropteridine reductase deficiency
HGVS variant names NC 000004.11:g.17510986A>G
ClinVar review status no assertion criteria provided
Clinical Significance Pathogenic
Variant type single nucleotide variant
Sequence Ontology for variant type SO:0001483
Variant clinical sources reported ClinGen:CA114326|OMIM:612676.0004|UniProtKB:P09417#VAR 006961
Gene symbol:Gene id. QDPR:5860
Molecular consequence SO:0001583|missense variant, SO:0001619|non-coding transcript variant, SO:0001627|intron variant
Allele origin germline
dbSNP ID 104893865
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