View genomic variant #0000001656

Chromosome	1
Allele	Unknown
Affects function (as reported)	Affects function
Affects function (by curator)	Affects function
Type	subst
DNA change (genomic) (Relative to hg19 / GRCh37)	g.156107547C>T
Published as	-
GERP	5.600
Segregation	-
DB-ID	LMNA_000007
MSCV	MSCV_0001656
dbSNP ID	rs80338938
Frequency	-
Sources	; clinvar;
Reference	10580070;20301717
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.

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.

Legend

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	0000001656	+/+	c.1698+13C>T	p.(=)	-	-	-	-	r.(=)	-

Legend

ClinVar @ MSeqDR
RCVaccession	RCV000015574; RCV000057044; RCV000705473; RCV001189216;
Chromosome	1:156107547..156107547
ClinVar Allele ID	29524
Disease database name and identifier	MONDO:MONDO:0018993, MedGen:C0270914, Orphanet:64746\|MedGen:CN517202\|Human Phenotype Ontology:HP:0001638, MONDO:MONDO:0004994, MedGen:C0878544, Orphanet:167848\|MONDO:MONDO:0007269, MedGen:C1449563, OMIM:115200, Orphanet:300751
ClinVar preferred disease name	Charcot-Marie-Tooth disease type 2\|not provided\|Cardiomyopathy\|Dilated cardiomyopathy 1A
HGVS variant names	NC 000001.10:g.156107547C>A
ClinVar review status	criteria provided, conflicting interpretations
Clinical Significance	Conflicting interpretations of pathogenicity
Conflicting clinical significance	Pathogenic(1)\|Uncertain significance(3)
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Variant clinical sources reported	ClinGen:CA017694\|OMIM:150330.0009
Gene symbol:Gene id.	LMNA:4000
Molecular consequence	SO:0001583\|missense variant, SO:0001627\|intron variant
Allele origin	germline
dbSNP ID	80338938
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV000057045; RCV000790249; RCV001176130; RCV001854169; RCV002504958;
Chromosome 1:156107547..156107547
ClinVar Allele ID 77508
Disease database name and identifier MONDO:MONDO:0015626, MedGen:C0007959, OMIM:PS118220, Orphanet:166|MONDO:MONDO:0018993, MedGen:C0270914, Orphanet:64746|MedGen:CN517202|Human Phenotype Ontology:HP:0001638, MONDO:MONDO:0004994, MedGen:C0878544, Orphanet:167848|MONDO:MONDO:0008915, MedGen:C0796031, OMIM:212112, Orphanet:2229|MONDO:MONDO:0007269, MedGen:C1449563, OMIM:115200, Orphanet:300751|MONDO:MONDO:0009557, MedGen:C5399785, OMIM:248370, Orphanet:2457, Orphanet:90153|MONDO:MONDO:0007906, MedGen:C1720860, OMIM:151660, Orphanet:2348|MONDO:MONDO:0011569, MedGen:C1854154, OMIM:605588, Orphanet:98856|MONDO:MONDO:0021569, MedGen:C0410190, OMIM:181350, Orphanet:261, Orphanet:264|MONDO:MONDO:0013178, MedGen:C2750785, OMIM:613205, Orphanet:157973|MONDO:MONDO:0014676, MedGen:C2750035, OMIM:616516, Orphanet:261|MONDO:MONDO:0030781, MedGen:C5676942, OMIM:619793|MONDO:MONDO:0012417, MedGen:C1857829, OMIM:610140, Orphanet:168796|MONDO:MONDO:0008310, MedGen:C0033300, OMIM:176670, Orphanet:740
ClinVar preferred disease name Charcot-Marie-Tooth disease|Charcot-Marie-Tooth disease type 2|not provided|Cardiomyopathy|Dilated cardiomyopathy-hypergonadotropic hypogonadism syndrome|Dilated cardiomyopathy 1A|Mandibuloacral dysplasia with type A lipodystrophy|Familial partial lipodystrophy, Dunnigan type|Charcot-Marie-Tooth disease type 2B1|Benign scapuloperoneal muscular dystrophy with cardiomyopathy|Congenital muscular dystrophy due to LMNA mutation|Emery-Dreifuss muscular dystrophy 3, autosomal recessive|Restrictive dermopathy 2|Heart-hand syndrome, Slovenian type|Hutchinson-Gilford syndrome
HGVS variant names NC 000001.10:g.156107547C>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
Variant clinical sources reported ClinGen:CA017701
Gene symbol:Gene id. LMNA:4000
Molecular consequence SO:0001583|missense variant, SO:0001627|intron variant
Allele origin germline
dbSNP ID 80338938
Variant Flags
:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV000249124; RCV000725840; RCV001191556; RCV001300467; RCV003333038; RCV003416104;
Chromosome 1:156107547..156107548
ClinVar Allele ID 196485
Disease database name and identifier MedGen:CN230736|.|MedGen:C3661900|Human Phenotype Ontology:HP:0001638, MONDO:MONDO:0004994, MedGen:C0878544, Orphanet:167848|MONDO:MONDO:0008915, MedGen:C0796031, OMIM:212112, Orphanet:2229|MONDO:MONDO:0018993, MedGen:C0270914, Orphanet:64746
ClinVar preferred disease name Cardiovascular phenotype|LMNA-related condition|not provided|Cardiomyopathy|Dilated cardiomyopathy-hypergonadotropic hypogonadism syndrome|Charcot-Marie-Tooth disease type 2
HGVS variant names NC 000001.10:g.156107547 156107548delinsTC
ClinVar review status criteria provided, conflicting interpretations
Clinical Significance Conflicting interpretations of pathogenicity
Conflicting clinical significance Pathogenic(1)|Uncertain significance(6)
Variant type Indel
Sequence Ontology for variant type SO:1000032
Variant clinical sources reported ClinGen:CA017680
Gene symbol:Gene id. LMNA:4000
Molecular consequence SO:0001583|missense variant, SO:0001627|intron variant
Allele origin germline
dbSNP ID 794728612
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