View genomic variant #0000001646

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

1 entry on 1 page. Showing entry 1.

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Gene	Transcript ID	Transcript	Variant ID	Affects function	DNA change (cDNA)	Protein	GVS function	Position	Exon	PolyPhen	RNA change	SIFT
LMNA	00003231	NM_170707.3	0000001646	+?/+?	c.1146C>T	p.(=)	synonymous_variant	-	6/12	-	r.(=)	-

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ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000041309; RCV000057239; RCV000468865; RCV000620488; RCV001775074;
Chromosome	1:156105901..156105901
ClinVar Allele ID	57196
Disease database name and identifier	MedGen:CN230736|MONDO:MONDO:0018993, MedGen:C0270914, Orphanet:64746|MedGen:C3661900|MONDO:MONDO:0007269, MedGen:C1449563, OMIM:115200, Orphanet:300751|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|MONDO:MONDO:0019056, MeSH:D009468, MedGen:C0027868, Orphanet:68381
ClinVar preferred disease name	Cardiovascular phenotype|Charcot-Marie-Tooth disease type 2|not provided|Dilated cardiomyopathy 1A|Primary dilated cardiomyopathy|Neuromuscular disease
HGVS variant names	NC 000001.10:g.156105901C>T
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:CA016690
Gene symbol:Gene id.	LMNA:4000
Molecular consequence	SO:0001819|synonymous variant
Allele origin	germline
dbSNP ID	57508089
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000503663; RCV002281642;
Chromosome	1:156105902..156105904
ClinVar Allele ID	427651
Disease database name and identifier	MONDO:MONDO:0021569, MedGen:C0410190, OMIM:181350, Orphanet:261, Orphanet:264|Human Phenotype Ontology:HP:0003544, Human Phenotype Ontology:HP:0003560, Human Phenotype Ontology:HP:0003806, MONDO:MONDO:0020121, MeSH:D009136, MedGen:C0026850, Orphanet:98473
ClinVar preferred disease name	Benign scapuloperoneal muscular dystrophy with cardiomyopathy|Muscular dystrophy
HGVS variant names	NC 000001.10:g.156105902GAG[2]
ClinVar review status	criteria provided, single submitter
Clinical Significance	Likely pathogenic
Variant type	Microsatellite
Sequence Ontology for variant type	SO:0000289
Variant clinical sources reported	ClinGen:CA645372475
Gene symbol:Gene id.	LMNA:4000
Molecular consequence	SO:0001822|inframe deletion
Allele origin
dbSNP ID	1553265761
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