View genomic variant #0000015835

Variant on transcripts

Legend

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.

10 per page 25 per page 50 per page 100 per page 250 per page 500 per page 1000 per page

Legend

Gene	Transcript ID	Transcript	Variant ID	Affects function	DNA change (cDNA)	Protein	GVS function	Position	Exon	PolyPhen	RNA change	SIFT
RET	00003304	NM_020975.4	0000015835	./.	c.3116C>T	p.(Pro1039Leu)	-	-	-	-	r.(?)	-

10 per page 25 per page 50 per page 100 per page 250 per page 500 per page 1000 per page

Legend

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV002591722;
Chromosome	10:43622099..43622099
ClinVar Allele ID	1919492
Disease database name and identifier	MONDO:MONDO:0019003, MedGen:C4048306, Orphanet:653
ClinVar preferred disease name	Multiple endocrine neoplasia, type 2
HGVS variant names	NC 000010.10:g.43622099C>G
ClinVar review status	criteria provided, single submitter
Clinical Significance	Uncertain significance
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Gene symbol:Gene id.	RET:5979
Molecular consequence	SO:0001583|missense variant
Allele origin	germline
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000014975; RCV000148783; RCV000410425; RCV000411688; RCV000563865; RCV000704911; RCV002490367; RCV003398513;
Chromosome	10:43622099..43622099
Allele frequencies from ExAC	0.00002
Allele frequencies from TGP	0.00020
ClinVar Allele ID	28987
Disease database name and identifier	MONDO:MONDO:0008082, MeSH:D018814, MedGen:C0025269, OMIM:162300, Orphanet:247709, Orphanet:653|MONDO:MONDO:0007723, MedGen:C3888239, OMIM:142623, Orphanet:388|MONDO:MONDO:0008234, MeSH:D018813, MedGen:C0025268, OMIM:171400, Orphanet:247698, Orphanet:653|Human Phenotype Ontology:HP:0002666, MONDO:MONDO:0008233, MedGen:C0031511, OMIM:171300, Orphanet:29072|MONDO:MONDO:0007958, MedGen:C1833921, OMIM:155240, Orphanet:653, Orphanet:99361|MONDO:MONDO:0015356, MeSH:D009386, MedGen:C0027672, Orphanet:140162|MedGen:CN169374|MONDO:MONDO:0019003, MedGen:C4048306, Orphanet:653|Human Phenotype Ontology:HP:0002029, Human Phenotype Ontology:HP:0002030, Human Phenotype Ontology:HP:0002251, Human Phenotype Ontology:HP:0002606, Human Phenotype Ontology:HP:0004391, MONDO:MONDO:0018309, MeSH:D006627, MedGen:C0019569, OMIM:PS142623, Orphanet:388
ClinVar preferred disease name	Multiple endocrine neoplasia, type 2b|Hirschsprung disease, susceptibility to, 1|Multiple endocrine neoplasia, type 2a|Pheochromocytoma|Familial medullary thyroid carcinoma|Hereditary cancer-predisposing syndrome|not specified|Multiple endocrine neoplasia, type 2|Aganglionic megacolon
HGVS variant names	NC 000010.10:g.43622099C>T
ClinVar review status	criteria provided, conflicting interpretations
Clinical Significance	Conflicting interpretations of pathogenicity
Conflicting clinical significance	Uncertain significance(5)|Likely benign(1)
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Variant clinical sources reported	ClinGen:CA009200|OMIM:164761.0046|UniProtKB:P07949#VAR 018157
Gene symbol:Gene id.	RET:5979
Molecular consequence	SO:0001583|missense variant
Allele origin	germline
dbSNP ID	79853121
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