View genomic variant #0000001650

Variant on transcripts

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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	0000001650	+/+	c.1445G>A	p.(Arg482Gln)	missense_variant	-	8/12	benign(0.01)	r.(?)	deleterious(0.04)

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ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000015580; RCV000057300; RCV001098782; RCV001097055; RCV001097056; RCV001098784; RCV001098785; RCV001098786; RCV001098787; RCV001098783; RCV001098788;
Chromosome	1:156106776..156106776
ClinVar Allele ID	29529
Disease database name and identifier	MedGen:CN239184|MedGen:C3661900|MONDO:MONDO:0016830, MedGen:C0410189, OMIM:PS310300, Orphanet:261|MONDO:MONDO:0011569, MedGen:C1854154, OMIM:605588, Orphanet:98856|MONDO:MONDO:0008310, MedGen:C0033300, OMIM:176670, Orphanet:740|MONDO:MONDO:0013178, MedGen:C2750785, OMIM:613205, Orphanet:157973|MONDO:MONDO:0007269, MedGen:C1449563, OMIM:115200, Orphanet:300751|MONDO:MONDO:0007906, MedGen:C1720860, OMIM:151660, Orphanet:2348|MONDO:MONDO:0009557, MedGen:C5399785, OMIM:248370, Orphanet:2457, Orphanet:90153|MONDO:MONDO:0021569, MedGen:C0410190, OMIM:181350, Orphanet:261, Orphanet:264|MONDO:MONDO:0031213, MedGen:C0406585, OMIM:PS275210, Orphanet:1662
ClinVar preferred disease name	Lipoatrophy with Diabetes, Hepatic Steatosis, Hypertrophic Cardiomyopathy, and Leukomelanodermic Papules|not provided|Emery-Dreifuss muscular dystrophy|Charcot-Marie-Tooth disease type 2B1|Hutchinson-Gilford syndrome|Congenital muscular dystrophy due to LMNA mutation|Dilated cardiomyopathy 1A|Familial partial lipodystrophy, Dunnigan type|Mandibuloacral dysplasia with type A lipodystrophy|Benign scapuloperoneal muscular dystrophy with cardiomyopathy|Lethal tight skin contracture syndrome
HGVS variant names	NC 000001.10:g.156106776G>T
ClinVar review status	criteria provided, single submitter
Clinical Significance	Uncertain significance
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Variant clinical sources reported	ClinGen:CA017271|OMIM:150330.0012|UniProtKB:P02545#VAR 009991
Gene symbol:Gene id.	LMNA:4000
Molecular consequence	SO:0001583|missense variant
Allele origin	germline
dbSNP ID	11575937
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