View genomic variant #0000003620

Chromosome	X
Allele	Unknown
Affects function (as reported)	Affects function
Affects function (by curator)	Affects function
Type	subst
DNA change (genomic) (Relative to hg19 / GRCh37)	g.18600062G>T
Published as	-
GERP	6.070
Segregation	-
DB-ID	CDKL5_000003
MSCV	MSCV_0003620
dbSNP ID	rs122460157
Frequency	-
Sources	; clinvar;
Reference	15499549
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
CDKL5	00000603	NM_001037343.1	0000003620	+/+	-	8/22	c.455G>T	p.(Cys152Phe)	probably_damaging(0.951)	missense_variant	-	deleterious(0)
CDKL5	00000602	NM_003159.2	0000003620	+/+	-	8/22	c.455G>T	p.(Cys152Phe)	probably_damaging(0.951)	missense_variant	-	deleterious(0)

Legend

ClinVar @ MSeqDR
RCVaccession	RCV000585869; RCV002530871;
Chromosome	X:18600062..18600062
ClinVar Allele ID	486784
Disease database name and identifier	MONDO:MONDO:0010396, MedGen:C4750718, OMIM:300672, Orphanet:1934, Orphanet:3451, Orphanet:505652\|MedGen:CN128785
ClinVar preferred disease name	Developmental and epileptic encephalopathy, 2\|Angelman syndrome-like
HGVS variant names	NC 000023.10:g.18600062G>A
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
Variant clinical sources reported	ClinGen:CA412351052
Gene symbol:Gene id.	CDKL5:6792
Molecular consequence	SO:0001583\|missense variant
Allele origin
dbSNP ID	122460157
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV000012251; RCV000133370;
Chromosome X:18600062..18600062
ClinVar Allele ID 26535
Disease database name and identifier MONDO:MONDO:0010396, MedGen:C4750718, OMIM:300672, Orphanet:1934, Orphanet:3451, Orphanet:505652|MONDO:MONDO:0017746, MedGen:C2748910, Orphanet:3095
ClinVar preferred disease name Developmental and epileptic encephalopathy, 2|Atypical Rett syndrome
HGVS variant names NC 000023.10:g.18600062G>T
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:CA121515|OMIM:300203.0003|RettBASE (CDKL5):7|UniProtKB:O76039#VAR 023560
Gene symbol:Gene id. CDKL5:6792
Molecular consequence SO:0001583|missense variant
Allele origin
dbSNP ID 122460157
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