View genomic variant #0000000065

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
NRAS	00003322	NM_002524.4	0000000065	./.	c.182A>C	p.(Gln61Pro)	missense_variant	-	3/7	possibly_damaging(0.713)	r.(?)	deleterious(0)

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ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000014914; RCV000032847; RCV000037574; RCV000114744; RCV000114745; RCV000148032; RCV000413804; RCV000422078; RCV000422278; RCV000430407; RCV000430593; RCV000435687; RCV000420832; RCV000438052; RCV000419710; RCV000440367; RCV000424960; RCV000424455; RCV000424721; RCV00044;
Chromosome	1:115256529..115256529
ClinVar Allele ID	28939
Disease database name and identifier	Human Phenotype Ontology:HP:0002861, Human Phenotype Ontology:HP:0002887, Human Phenotype Ontology:HP:0006777, Human Phenotype Ontology:HP:0007474, MONDO:MONDO:0005105, MeSH:D008545, MedGen:C0025202|Human Phenotype Ontology:HP:0033770, MONDO:MONDO:0005036, MedGen:C0278701|Human Phenotype Ontology:HP:0002889, Human Phenotype Ontology:HP:0006744, Human Phenotype Ontology:HP:0006759, MONDO:MONDO:0006639, MeSH:D018268, MedGen:C0206686, Orphanet:1501|MedGen:C0153574|Human Phenotype Ontology:HP:0100630, MONDO:MONDO:0005375, MeSH:D009303, MedGen:C0027439|MONDO:MONDO:0006046, MedGen:C0279663|Human Phenotype Ontology:HP:0100834, MONDO:MONDO:0005335, MeSH:D015179, MedGen:C0009404|Human Phenotype Ontology:HP:0005600, Human Phenotype Ontology:HP:0005604, MONDO:MONDO:0044792, MedGen:C1842036, OMIM:137550, Orphanet:626|Human Phenotype Ontology:HP:0030692, MONDO:MONDO:0021211, MeSH:D001932, MedGen:C0006118|MONDO:MONDO:0009578, MedGen:C0544862, OMIM:249400, Orphanet:2481|MONDO:MONDO:0018177, MeSH:D005909, MedGen:C0017636, Orphanet:360|MedGen:C3661900|Human Phenotype Ontology:HP:0005550, Human Phenotype Ontology:HP:0006734, Human Phenotype Ontology:HP:0006760, MONDO:MONDO:0004948, MeSH:D015451, MedGen:C0023434, OMIM:151400, Orphanet:67038|Human Phenotype Ontology:HP:0010817, MONDO:MONDO:0008097, MedGen:C4552097, OMIM:163200, Orphanet:2612|Human Phenotype Ontology:HP:0012056, MONDO:MONDO:0005012, MeSH:C562393, MedGen:C0151779|Human Phenotype Ontology:HP:0001914, Human Phenotype Ontology:HP:0004808, Human Phenotype Ontology:HP:0004843, Human Phenotype Ontology:HP:0005516, Human Phenotype Ontology:HP:0006724, Human Phenotype Ontology:HP:0006728, MONDO:MONDO:0018874, MeSH:D015470, MedGen:C0023467, OMIM:601626, Orphanet:519|Human Phenotype Ontology:HP:0006775, MONDO:MONDO:0009693, MeSH:D009101, MedGen:C0026764, OMIM:254500, Orphanet:29073, Orphanet:85443|Human Phenotype Ontology:HP:0001402, Human Phenotype Ontology:HP:0002899, Human Phenotype Ontology:HP:0003007, Human Phenotype Ontology:HP:0006750, MONDO:MONDO:0007256, MedGen:C2239176, OMIM:114550, Orphanet:88673|Human Phenotype Ontology:HP:0010816, MONDO:MONDO:0008093, MedGen:C0334082, OMIM:162900, Orphanet:79414|Human Phenotype Ontology:HP:0030358, MONDO:MONDO:0005233, MeSH:D002289, MedGen:C0007131|Human Phenotype Ontology:HP:0011797, MedGen:C1336839, OMIM:605074, Orphanet:47044|Human Phenotype Ontology:HP:0030078, MONDO:MONDO:0005061, MeSH:D000077192, MedGen:C0152013|MONDO:MONDO:0008566, MedGen:C4225426, OMIM:188470|Human Phenotype Ontology:HP:0006740, MONDO:MONDO:0005611, MedGen:C0279680
ClinVar preferred disease name	Melanoma|Gastric adenocarcinoma|Adrenal cortex carcinoma|Malignant neoplasm of body of uterus|Neoplasia of the nasopharynx|Ovarian serous cystadenocarcinoma|Neoplasm of the large intestine|Large congenital melanocytic nevus|Neoplasm of brain|Neurocutaneous melanocytosis|Glioblastoma|not provided|Chronic lymphatic leukemia|Linear nevus sebaceous syndrome|Malignant melanoma of skin|Acute myeloid leukemia|Multiple myeloma|Hepatocellular carcinoma|Epidermal nevus|Non-small cell lung carcinoma|Papillary renal cell carcinoma type 1|Lung adenocarcinoma|Thyroid cancer, nonmedullary, 2|Transitional cell carcinoma of the bladder
HGVS variant names	NC 000001.10:g.115256529T>C
ClinVar review status	criteria provided, multiple submitters, no conflicts
Clinical Significance	Pathogenic
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Variant clinical sources reported	ClinGen:CA123618|OMIM:164790.0002|UniProtKB:P01111#VAR 006847
Gene symbol:Gene id.	NRAS:4893
Molecular consequence	SO:0001583|missense variant
Allele origin
dbSNP ID	11554290
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000291285; RCV000421496; RCV000427746; RCV000431592; RCV000444660; RCV000419053; RCV000419201; RCV000421291; RCV000420302; RCV000434604; RCV000437312; RCV000438468; RCV000444278; RCV000426654; RCV000428903; RCV000430000; RCV000432170; RCV000437545; RCV000439526; RCV00043;
Chromosome	1:115256529..115256529
ClinVar Allele ID	263939
Disease database name and identifier	MONDO:MONDO:0006046, MedGen:C0279663|Human Phenotype Ontology:HP:0100630, MONDO:MONDO:0005375, MeSH:D009303, MedGen:C0027439|Human Phenotype Ontology:HP:0100031, MONDO:MONDO:0015074, MeSH:D013964, MedGen:C0040136, Orphanet:100087|MedGen:C0153574|Human Phenotype Ontology:HP:0100834, MONDO:MONDO:0005335, MeSH:D015179, MedGen:C0009404|Human Phenotype Ontology:HP:0030692, MONDO:MONDO:0021211, MeSH:D001932, MedGen:C0006118|Human Phenotype Ontology:HP:0030078, MONDO:MONDO:0005061, MeSH:D000077192, MedGen:C0152013|MedGen:C3661900|Human Phenotype Ontology:HP:0006775, MONDO:MONDO:0009693, MeSH:D009101, MedGen:C0026764, OMIM:254500, Orphanet:29073, Orphanet:85443|Human Phenotype Ontology:HP:0001402, Human Phenotype Ontology:HP:0002899, Human Phenotype Ontology:HP:0003007, Human Phenotype Ontology:HP:0006750, MONDO:MONDO:0007256, MedGen:C2239176, OMIM:114550, Orphanet:88673|Human Phenotype Ontology:HP:0006740, MONDO:MONDO:0005611, MedGen:C0279680|Human Phenotype Ontology:HP:0002889, Human Phenotype Ontology:HP:0006744, Human Phenotype Ontology:HP:0006759, MONDO:MONDO:0006639, MeSH:D018268, MedGen:C0206686, Orphanet:1501|Human Phenotype Ontology:HP:0033770, MONDO:MONDO:0005036, MedGen:C0278701|Human Phenotype Ontology:HP:0011797, MedGen:C1336839, OMIM:605074, Orphanet:47044|MONDO:MONDO:0013186, MedGen:C2750732, OMIM:613224, Orphanet:648|Human Phenotype Ontology:HP:0002861, Human Phenotype Ontology:HP:0002887, Human Phenotype Ontology:HP:0006777, Human Phenotype Ontology:HP:0007474, MONDO:MONDO:0005105, MeSH:D008545, MedGen:C0025202|MONDO:MONDO:0018177, MeSH:D005909, MedGen:C0017636, Orphanet:360|Human Phenotype Ontology:HP:0005550, Human Phenotype Ontology:HP:0006734, Human Phenotype Ontology:HP:0006760, MONDO:MONDO:0004948, MeSH:D015451, MedGen:C0023434, OMIM:151400, Orphanet:67038|Human Phenotype Ontology:HP:0001914, Human Phenotype Ontology:HP:0004808, Human Phenotype Ontology:HP:0004843, Human Phenotype Ontology:HP:0005516, Human Phenotype Ontology:HP:0006724, Human Phenotype Ontology:HP:0006728, MONDO:MONDO:0018874, MeSH:D015470, MedGen:C0023467, OMIM:601626, Orphanet:519|Human Phenotype Ontology:HP:0012056, MONDO:MONDO:0005012, MeSH:C562393, MedGen:C0151779|Human Phenotype Ontology:HP:0030358, MONDO:MONDO:0005233, MeSH:D002289, MedGen:C0007131
ClinVar preferred disease name	Ovarian serous cystadenocarcinoma|Neoplasia of the nasopharynx|Thyroid tumor|Malignant neoplasm of body of uterus|Neoplasm of the large intestine|Neoplasm of brain|Lung adenocarcinoma|not provided|Multiple myeloma|Hepatocellular carcinoma|Transitional cell carcinoma of the bladder|Adrenal cortex carcinoma|Gastric adenocarcinoma|Papillary renal cell carcinoma type 1|Noonan syndrome 6|Melanoma|Glioblastoma|Chronic lymphatic leukemia|Acute myeloid leukemia|Malignant melanoma of skin|Non-small cell lung carcinoma
HGVS variant names	NC 000001.10:g.115256529T>G
ClinVar review status	criteria provided, single submitter
Clinical Significance	Pathogenic
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Variant clinical sources reported	ClinGen:CA10602732
Gene symbol:Gene id.	NRAS:4893
Molecular consequence	SO:0001583|missense variant
Allele origin
dbSNP ID	11554290
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000426087;
Chromosome	1:115256529..115256530
ClinVar Allele ID	363099
Disease database name and identifier	Human Phenotype Ontology:HP:0002861, Human Phenotype Ontology:HP:0002887, Human Phenotype Ontology:HP:0006777, Human Phenotype Ontology:HP:0007474, MONDO:MONDO:0005105, MeSH:D008545, MedGen:C0025202
ClinVar preferred disease name	Melanoma
HGVS variant names	NC 000001.10:g.115256529 115256530delinsCT
ClinVar review status	no assertion criteria provided
Clinical Significance	Likely pathogenic
Variant type	Indel
Sequence Ontology for variant type	SO:1000032
Variant clinical sources reported	ClinGen:CA16602673
Gene symbol:Gene id.	NRAS:4893
Molecular consequence	SO:0001583|missense variant
Allele origin	somatic
dbSNP ID	1057519834
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