View genomic variant #0000000278

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
HRAS	00003315	NM_176795.3	0000000278	./.	c.34G>A	p.(Gly12Ser)	missense_variant,NMD_transcript_variant	-	2/7	probably_damaging(0.993)	r.(?)	deleterious(0.02)

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ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000421560; RCV000431895; RCV002230756;
Chromosome	11:534289..534289
ClinVar Allele ID	362840
Disease database name and identifier	Human Phenotype Ontology:HP:0100031, MONDO:MONDO:0015074, MeSH:D013964, MedGen:C0040136, Orphanet:100087|MONDO:MONDO:0009026, MedGen:C0587248, OMIM:218040, Orphanet:3071|Human Phenotype Ontology:HP:0100834, MONDO:MONDO:0005335, MeSH:D015179, MedGen:C0009404
ClinVar preferred disease name	Thyroid tumor|Costello syndrome|Neoplasm of the large intestine
HGVS variant names	NC 000011.9:g.534289C>G
ClinVar review status	criteria provided, single submitter
Clinical Significance	Likely pathogenic
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Variant clinical sources reported	ClinGen:CA16602439
Gene symbol:Gene id.	HRAS:3265|LRRC56:115399
Molecular consequence	SO:0001583|missense variant, SO:0001623|5 prime UTR variant
Allele origin
dbSNP ID	104894229
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000013436; RCV000013435; RCV000022796; RCV000029209; RCV000081295; RCV000149828; RCV000419709; RCV000420366; RCV000422656; RCV000423310; RCV000424896; RCV000427772; RCV000430011; RCV000417494; RCV000432984; RCV000422253; RCV000440237; RCV000430608; RCV000425542; RCV00043;
Chromosome	11:534289..534289
ClinVar Allele ID	27641
Disease database name and identifier	MONDO:MONDO:0006485, MedGen:C0280630|MeSH:C538614, MedGen:C1336078|Human Phenotype Ontology:HP:0032241, MONDO:MONDO:0021230, MeSH:D002583, MedGen:C0007873|MONDO:MONDO:0005082, MedGen:C0007112|MONDO:MONDO:0004971, MeSH:D003528, MedGen:C0010606|MedGen:C0153574|Human Phenotype Ontology:HP:0100031, MONDO:MONDO:0015074, MeSH:D013964, MedGen:C0040136, Orphanet:100087|Human Phenotype Ontology:HP:0100630, MONDO:MONDO:0005375, MeSH:D009303, MedGen:C0027439|MONDO:MONDO:0006046, MedGen:C0279663|MONDO:MONDO:0023644, MedGen:C0220641|Human Phenotype Ontology:HP:0100834, MONDO:MONDO:0005335, MeSH:D015179, MedGen:C0009404|MONDO:MONDO:0020297, MedGen:C5681679, Orphanet:98733|MedGen:CN230736|.|Human Phenotype Ontology:HP:0033770, MONDO:MONDO:0005036, MedGen:C0278701|MeSH:D030342, MedGen:C0950123|MONDO:MONDO:0018177, MeSH:D005909, MedGen:C0017636, Orphanet:360|Human Phenotype Ontology:HP:0002859, MONDO:MONDO:0005212, MeSH:D012208, MedGen:C0035412, Orphanet:780|Human Phenotype Ontology:HP:0006725, MONDO:MONDO:0006047, MedGen:C0281361|MONDO:MONDO:0019311, MedGen:C0343114, Orphanet:79414|Human Phenotype Ontology:HP:0011459, MONDO:MONDO:0019086, MedGen:C0152018, Orphanet:70482|Human Phenotype Ontology:HP:0010623, Human Phenotype Ontology:HP:0100013, MONDO:MONDO:0021100, MeSH:D001943, MedGen:C1458155|MedGen:C3661900|MONDO:MONDO:0021060, MedGen:C5555857, Orphanet:536391|Human Phenotype Ontology:HP:0010815, MedGen:C3854181|MedGen:C3277679|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:0012056, MONDO:MONDO:0005012, MeSH:C562393, MedGen:C0151779|MONDO:MONDO:0018881, MeSH:D009190, MedGen:C3463824, OMIM:614286, Orphanet:52688|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|MONDO:MONDO:0008104, MedGen:C4551602, OMIM:163950, Orphanet:648|MONDO:MONDO:0009026, MedGen:C0587248, OMIM:218040, Orphanet:3071|MONDO:MONDO:0800299, MedGen:C1968782|Human Phenotype Ontology:HP:0030078, MONDO:MONDO:0005061, MeSH:D000077192, MedGen:C0152013|MONDO:MONDO:0010150, MeSH:D000077195, MedGen:C1168401, OMIM:275355, Orphanet:67037|Human Phenotype Ontology:HP:0006739, Human Phenotype Ontology:HP:0007614, MONDO:MONDO:0002529, MedGen:C0553723|Human Phenotype Ontology:HP:0006740, MONDO:MONDO:0005611, MedGen:C0279680|.
ClinVar preferred disease name	Uterine carcinosarcoma|Papillary renal cell carcinoma, sporadic|Neoplasm of uterine cervix|Prostate adenocarcinoma|Adenoid cystic carcinoma|Malignant neoplasm of body of uterus|Thyroid tumor|Neoplasia of the nasopharynx|Ovarian serous cystadenocarcinoma|Lip and oral cavity carcinoma|Neoplasm of the large intestine|Noonan syndrome and Noonan-related syndrome|Cardiovascular phenotype|HRAS-related condition|Gastric adenocarcinoma|Inborn genetic diseases|Glioblastoma|Rhabdomyosarcoma|Pancreatic adenocarcinoma|Wooly hair nevus|Esophageal carcinoma|Breast neoplasm|not provided|RASopathy|Nevus sebaceous|Epidermal nevus with urothelial cancer, somatic|Acute myeloid leukemia|Multiple myeloma|Malignant melanoma of skin|Myelodysplastic syndrome|Hepatocellular carcinoma|Epidermal nevus|Noonan syndrome 1|Costello syndrome|Myopathy, congenital, with excess of muscle spindles|Lung adenocarcinoma|Squamous cell carcinoma of the head and neck|Squamous cell carcinoma of the skin|Transitional cell carcinoma of the bladder|See cases
HGVS variant names	NC 000011.9:g.534289C>T
ClinVar review status	reviewed by expert panel
Clinical Significance	Pathogenic
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Variant clinical sources reported	ClinGen:CA122549|OMIM:190020.0003|UniProtKB:P01112#VAR 006837
Gene symbol:Gene id.	HRAS:3265|LRRC56:115399
Molecular consequence	SO:0001583|missense variant, SO:0001623|5 prime UTR variant
Allele origin
dbSNP ID	104894229
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