View genomic variant #0000001686

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.

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

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

Position: Position of variant in coding DNA sequence; note that coding DNA position can also be derived from the variant description.

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.

PolyPhen: Effect of variant, predicted by PolyPhen.
All options:

• benign = Benign
• possiblyDamaging = Possibly damaging
• probablyDamaging = Probably damaging
• noPrediction = No prediction

RNA change: Description of variant at RNA level (following HGVS recommendations).

• r.123c>u
• r.? = unknown
• r.(?) = RNA not analysed but probably transcribed copy of DNA variant
• r.spl? = RNA not analysed but variant probably affects splicing
• r.(spl?) = RNA not analysed but variant may affect splicing
• r.0? = change expected to abolish transcription

SIFT: SIFT Annotation

2 entries on 1 page. Showing entries 1 - 2.

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Gene	Transcript ID	Transcript	Variant ID	Affects function	DNA change (cDNA)	Protein	GVS function	Position	Exon	PolyPhen	RNA change	SIFT
TNNT2	00003241	NM_000364.2	0000001686	+/+	c.650_652del	p.(Lys217del)	-	-	-	-	r.(?)	-
TNNT2	00003346	NM_000364.3	0000001686	+/+	c.650_652del	p.(Lys217del)	-	-	-	-	r.(?)	-

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ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000036607; RCV000223828; RCV000211868; RCV000247384; RCV000524543; RCV001798105; RCV002051803; RCV003450713;
Chromosome	1:201331099..201331101
ClinVar Allele ID	52828
Disease database name and identifier	MedGen:CN230736|MedGen:C3661900|MONDO:MONDO:0011095, MedGen:C1832243, OMIM:601494, Orphanet:154, Orphanet:54260|MONDO:MONDO:0012900, MedGen:C2676271, OMIM:612422, Orphanet:75249|MONDO:MONDO:0007266, MedGen:C1861864, OMIM:115195|Human Phenotype Ontology:HP:0001638, MONDO:MONDO:0004994, MedGen:C0878544, Orphanet:167848|EFO:EFO 0000407, Human Phenotype Ontology:HP:0001644, Human Phenotype Ontology:HP:0001725, Human Phenotype Ontology:HP:0005159, Human Phenotype Ontology:HP:0200130, MONDO:MONDO:0005021, MeSH:D002311, MedGen:C0007193, Orphanet:217604
ClinVar preferred disease name	Cardiovascular phenotype|not provided|Dilated cardiomyopathy 1D|Cardiomyopathy, familial restrictive, 3|Hypertrophic cardiomyopathy 2|Cardiomyopathy|Primary dilated cardiomyopathy
HGVS variant names	NC 000001.10:g.201331100CTT[3]
ClinVar review status	criteria provided, multiple submitters, no conflicts
Clinical Significance	Pathogenic/Likely pathogenic
Variant type	Microsatellite
Sequence Ontology for variant type	SO:0000289
Variant clinical sources reported	ClinGen:CA006429|OMIM:191045.0006
Gene symbol:Gene id.	TNNT2:7139
Molecular consequence	SO:0001822|inframe deletion
Allele origin
dbSNP ID	45578238
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV001037495; RCV001188983; RCV002286801; RCV003455153; RCV003455152; RCV003455154;
Chromosome	1:201331101..201331101
Allele frequencies from ExAC	0.00001
Allele frequencies from TGP	0.00020
ClinVar Allele ID	823225
Disease database name and identifier	MONDO:MONDO:0011095, MedGen:C1832243, OMIM:601494, Orphanet:154, Orphanet:54260|MONDO:MONDO:0012900, MedGen:C2676271, OMIM:612422, Orphanet:75249|MedGen:C3661900|MONDO:MONDO:0007266, MedGen:C1861864, OMIM:115195|Human Phenotype Ontology:HP:0001638, MONDO:MONDO:0004994, MedGen:C0878544, Orphanet:167848
ClinVar preferred disease name	Dilated cardiomyopathy 1D|Cardiomyopathy, familial restrictive, 3|not provided|Hypertrophic cardiomyopathy 2|Cardiomyopathy
HGVS variant names	NC 000001.10:g.201331101T>A
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.	TNNT2:7139
Molecular consequence	SO:0001583|missense variant
Allele origin	germline
dbSNP ID	190805300
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