View genomic variant #0000000468

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
KRAS	00003332	NM_033360.2	0000000468	./.	c.35G>C	p.(=)	missense_variant	-	2/6	possibly_damaging(0.773)	r.(=)	deleterious(0.02)

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ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000038266; RCV000423968; RCV000441134; RCV000434342; RCV000443636; RCV000984117; RCV001355876; RCV001374446; RCV003398604;
Chromosome	12:25398284..25398284
ClinVar Allele ID	54289
Disease database name and identifier	.|Human Phenotype Ontology:HP:0100834, MONDO:MONDO:0005335, MeSH:D015179, MedGen:C0009404|MONDO:MONDO:0005411, MedGen:C0153452|MedGen:C3661900|Human Phenotype Ontology:HP:0100615, MONDO:MONDO:0021068, MeSH:D010051, MedGen:C0919267, OMIM:167000|Human Phenotype Ontology:HP:0100723, MONDO:MONDO:0011719, MeSH:D046152, MedGen:C0238198, OMIM:606764, Orphanet:44890|Human Phenotype Ontology:HP:0006775, MONDO:MONDO:0009693, MeSH:D009101, MedGen:C0026764, OMIM:254500, Orphanet:29073, Orphanet:85443|Human Phenotype Ontology:HP:0030358, MONDO:MONDO:0005233, MeSH:D002289, MedGen:C0007131|Human Phenotype Ontology:HP:0030078, MONDO:MONDO:0005061, MeSH:D000077192, MedGen:C0152013
ClinVar preferred disease name	KRAS-related condition|Neoplasm of the large intestine|Gallbladder cancer|not provided|Neoplasm of ovary|Gastrointestinal stroma tumor|Multiple myeloma|Non-small cell lung carcinoma|Lung adenocarcinoma
HGVS variant names	NC 000012.11:g.25398284C>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:CA135567|UniProtKB:P01116#VAR 036305
Gene symbol:Gene id.	KRAS:3845
Molecular consequence	SO:0001583|missense variant
Allele origin
dbSNP ID	121913529
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000013411; RCV000022799; RCV000029214; RCV000029215; RCV000144969; RCV000144970; RCV000150896; RCV000150897; RCV000272938; RCV000426369; RCV000425250; RCV000433573; RCV000443973; RCV000548006; RCV000585796; RCV000662266; RCV000856666; RCV001799604; RCV001839445; RCV00250;
Chromosome	12:25398284..25398284
Allele frequencies from ExAC	0.00002
ClinVar Allele ID	27621
Disease database name and identifier	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|MONDO:MONDO:0006193, MedGen:C1516855|MONDO:MONDO:0006096, MedGen:C0349579|MONDO:MONDO:0013074, MedGen:C0406612, OMIM:613001, Orphanet:2396|Human Phenotype Ontology:HP:0012126, MONDO:MONDO:0001056, MeSH:D013274, MedGen:C0024623, OMIM:613659|Human Phenotype Ontology:HP:0012209, MONDO:MONDO:0011908, MedGen:C0349639, OMIM:607785, Orphanet:86834|MedGen:C4302356|.|MedGen:C3661900|MONDO:MONDO:0021060, MedGen:C5555857, Orphanet:536391|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: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|MONDO:MONDO:0005192, MeSH:C562463, MedGen:C0235974, OMIM:260350, Orphanet:1333, Orphanet:217074|Human Phenotype Ontology:HP:0100615, MONDO:MONDO:0021068, MeSH:D010051, MedGen:C0919267, OMIM:167000|Human Phenotype Ontology:HP:0002408, MONDO:MONDO:0007154, MedGen:C0917804, OMIM:108010, Orphanet:46724|MONDO:MONDO:0005138, MedGen:C0684249|Human Phenotype Ontology:HP:0010816, MONDO:MONDO:0008093, MedGen:C0334082, OMIM:162900, Orphanet:79414|MONDO:MONDO:0020783, MedGen:C4747394, OMIM:608354, Orphanet:137667, Orphanet:90307|Human Phenotype Ontology:HP:0030358, MONDO:MONDO:0005233, MeSH:D002289, MedGen:C0007131|MONDO:MONDO:0013767, MedGen:C2674723, OMIM:614470, Orphanet:268114
ClinVar preferred disease name	Thyroid tumor|Neoplasm of the large intestine|Endometrial hyperplasia without atypia|Atypical endometrial hyperplasia|Encephalocraniocutaneous lipomatosis|Stomach cancer|Juvenile myelomonocytic leukemia|Primary low grade serous adenocarcinoma of ovary|Vascular Tumors Including Pyogenic Granuloma|not provided|RASopathy|Nevus sebaceous|Linear nevus sebaceous syndrome|Acute myeloid leukemia|Carcinoma of pancreas|Neoplasm of ovary|Cerebral arteriovenous malformation|Lung carcinoma|Epidermal nevus|Capillary malformation-arteriovenous malformation 1|Non-small cell lung carcinoma|Autoimmune lymphoproliferative syndrome type 4
HGVS variant names	NC 000012.11:g.25398284C>T
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:CA122538|OMIM:190070.0005|OMIM:190070.0025|UniProtKB:P01116#VAR 016026
Gene symbol:Gene id.	KRAS:3845
Molecular consequence	SO:0001583|missense variant
Allele origin
dbSNP ID	121913529
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