View genomic variant #0000000267

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	0000000267	./.	c.37G>T	p.(Gly13Cys)	missense_variant,NMD_transcript_variant	-	2/7	probably_damaging(0.999)	r.(?)	deleterious(0.05)

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ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000029212; RCV000029213; RCV000032852; RCV000173005; RCV000173006; RCV000424371; RCV000431824; RCV000418725; RCV000420422; RCV000420481; RCV000419344; RCV000432361; RCV000439826; RCV000422625; RCV000427669; RCV000430065; RCV000430227; RCV000435072; RCV000437649; RCV00044;
Chromosome	11:534286..534286
ClinVar Allele ID	44227
Disease database name and identifier	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|.|MONDO:MONDO:0023644, MedGen:C0220641|MONDO:MONDO:0020297, MedGen:C5681679, Orphanet:98733|MedGen:C0153574|Human Phenotype Ontology:HP:0032241, MONDO:MONDO:0021230, MeSH:D002583, MedGen:C0007873|Human Phenotype Ontology:HP:0033770, MONDO:MONDO:0005036, MedGen:C0278701|Human Phenotype Ontology:HP:0100031, MONDO:MONDO:0015074, MeSH:D013964, MedGen:C0040136, Orphanet:100087|Human Phenotype Ontology:HP:0100834, MONDO:MONDO:0005335, MeSH:D015179, MedGen:C0009404|Human Phenotype Ontology:HP:0012056, MONDO:MONDO:0005012, MeSH:C562393, MedGen:C0151779|Human Phenotype Ontology:HP:0010816, MONDO:MONDO:0008093, MedGen:C0334082, OMIM:162900, Orphanet:79414|Human Phenotype Ontology:HP:0001790, MONDO:MONDO:0009369, MedGen:C0455988, OMIM:236750, Orphanet:363999|Human Phenotype Ontology:HP:0010815, MedGen:C3854181|Human Phenotype Ontology:HP:0010817, MONDO:MONDO:0008097, MedGen:C4552097, OMIM:163200, Orphanet:2612|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: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|MONDO:MONDO:0044656, MedGen:C1302848, Orphanet:497737|Human Phenotype Ontology:HP:0030359, MONDO:MONDO:0005097, MedGen:C0149782|Human Phenotype Ontology:HP:0030078, MONDO:MONDO:0005061, MeSH:D000077192, MedGen:C0152013|MONDO:MONDO:0009026, MedGen:C0587248, OMIM:218040, Orphanet:3071|Human Phenotype Ontology:HP:0006725, MONDO:MONDO:0006047, MedGen:C0281361|Human Phenotype Ontology:HP:0010623, Human Phenotype Ontology:HP:0100013, MONDO:MONDO:0021100, MeSH:D001943, MedGen:C1458155|MONDO:MONDO:0010150, MeSH:D000077195, MedGen:C1168401, OMIM:275355, Orphanet:67037|Human Phenotype Ontology:HP:0006740, MONDO:MONDO:0005611, MedGen:C0279680|Human Phenotype Ontology:HP:0006739, Human Phenotype Ontology:HP:0007614, MONDO:MONDO:0002529, MedGen:C0553723|.|.
ClinVar preferred disease name	Chronic lymphatic leukemia|cutaneous-skeletal hypophosphatemia syndrome|Lip and oral cavity carcinoma|Noonan syndrome and Noonan-related syndrome|Malignant neoplasm of body of uterus|Neoplasm of uterine cervix|Gastric adenocarcinoma|Thyroid tumor|Neoplasm of the large intestine|Malignant melanoma of skin|Epidermal nevus|Non-immune hydrops fetalis|Nevus sebaceous|Linear nevus sebaceous syndrome|Hepatocellular carcinoma|Acute myeloid leukemia|Multiple myeloma|Epidermolytic nevus|Squamous cell lung carcinoma|Lung adenocarcinoma|Costello syndrome|Pancreatic adenocarcinoma|Breast neoplasm|Squamous cell carcinoma of the head and neck|Transitional cell carcinoma of the bladder|Squamous cell carcinoma of the skin|NEVUS SPILUS, SOMATIC|SPITZ NEVUS, SOMATIC
HGVS variant names	NC 000011.9:g.534286C>G
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:CA129950|OMIM:190020.0017|UniProtKB:P01112#VAR 068817
Gene symbol:Gene id.	HRAS:3265|LRRC56:115399
Molecular consequence	SO:0001583|missense variant, SO:0001623|5 prime UTR variant
Allele origin
dbSNP ID	104894228
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000417857; RCV000422141; RCV000424171; RCV000427918; RCV000430707; RCV000430043; RCV000435549; RCV000440979; RCV000662270; RCV002524694;
Chromosome	11:534286..534286
ClinVar Allele ID	363202
Disease database name and identifier	.|Human Phenotype Ontology:HP:0010623, Human Phenotype Ontology:HP:0100013, MONDO:MONDO:0021100, MeSH:D001943, MedGen:C1458155|Human Phenotype Ontology:HP:0030078, MONDO:MONDO:0005061, MeSH:D000077192, MedGen:C0152013|Human Phenotype Ontology:HP:0002664, Human Phenotype Ontology:HP:0003008, Human Phenotype Ontology:HP:0006741, MONDO:MONDO:0005070, MeSH:D009369, MedGen:C0027651|MONDO:MONDO:0010150, MeSH:D000077195, MedGen:C1168401, OMIM:275355, Orphanet:67037|Human Phenotype Ontology:HP:0012056, MONDO:MONDO:0005012, MeSH:C562393, MedGen:C0151779|MONDO:MONDO:0009026, MedGen:C0587248, OMIM:218040, Orphanet:3071|Human Phenotype Ontology:HP:0006739, Human Phenotype Ontology:HP:0007614, MONDO:MONDO:0002529, MedGen:C0553723|Human Phenotype Ontology:HP:0030359, MONDO:MONDO:0005097, MedGen:C0149782|Human Phenotype Ontology:HP:0006740, MONDO:MONDO:0005611, MedGen:C0279680
ClinVar preferred disease name	Vascular Tumors Including Pyogenic Granuloma|Breast neoplasm|Lung adenocarcinoma|Neoplasm|Squamous cell carcinoma of the head and neck|Malignant melanoma of skin|Costello syndrome|Squamous cell carcinoma of the skin|Squamous cell lung carcinoma|Transitional cell carcinoma of the bladder
HGVS variant names	NC 000011.9:g.534286C>T
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:CA16602769
Gene symbol:Gene id.	HRAS:3265|LRRC56:115399
Molecular consequence	SO:0001583|missense variant, SO:0001623|5 prime UTR variant
Allele origin
dbSNP ID	104894228
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