View genomic variant #0000015821

Chromosome	10
Allele	Unknown
Affects function (as reported)	Probably affects function
Affects function (by curator)	Probably affects function
Type	-
DNA change (genomic) (Relative to hg19 / GRCh37)	g.43613840G>T
Published as	-
GERP	-
Segregation	-
DB-ID	RET_000048
MSCV	MSCV_0015821
dbSNP ID	-
Frequency	-
Sources	; clinvar;
Reference	-
Variant remarks	-
Genetic origin	-
Variant_disease	-
Average frequency (large NGS studies)	Variant not found in online data sets
Owner	LOVD

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.

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	0000015821	./.	c.2304G>T	p.(Glu768Asp)	-	-	-	-	r.(?)	-

Legend

ClinVar @ MSeqDR
RCVaccession	RCV003172684;
Chromosome	10:43613840..43613840
ClinVar Allele ID	2424041
Disease database name and identifier	MONDO:MONDO:0015356, MeSH:D009386, MedGen:C0027672, Orphanet:140162
ClinVar preferred disease name	Hereditary cancer-predisposing syndrome
HGVS variant names	NC 000010.10:g.43613840G>A
ClinVar review status	criteria provided, single submitter
Clinical Significance	Likely benign
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Gene symbol:Gene id.	RET:5979
Molecular consequence	SO:0001819\|synonymous variant
Allele origin	germline
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV000014956; RCV000021842; RCV000421871; RCV000426010; RCV000431893; RCV000432579; RCV000439063; RCV000445341; RCV001015022; RCV001811141; RCV002280861;
Chromosome 10:43613840..43613840
ClinVar Allele ID 28970
Disease database name and identifier Human Phenotype Ontology:HP:0002664, Human Phenotype Ontology:HP:0003008, Human Phenotype Ontology:HP:0006741, MONDO:MONDO:0005070, MeSH:D009369, MedGen:C0027651|Human Phenotype Ontology:HP:0002865, MONDO:MONDO:0015277, MeSH:C536914, MedGen:C0238462, Orphanet:1332|MONDO:MONDO:0015356, MeSH:D009386, MedGen:C0027672, Orphanet:140162|MedGen:C3661900|MONDO:MONDO:0019003, MedGen:C4048306, Orphanet:653|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|MONDO:MONDO:0007540, MeSH:D018761, MedGen:C0025267, OMIM:131100, Orphanet:652|MONDO:MONDO:0008234, MeSH:D018813, MedGen:C0025268, OMIM:171400, Orphanet:247698, Orphanet:653|MONDO:MONDO:0008082, MeSH:D018814, MedGen:C0025269, OMIM:162300, Orphanet:247709, Orphanet:653|MONDO:MONDO:0007958, MedGen:C1833921, OMIM:155240, Orphanet:653, Orphanet:99361|MONDO:MONDO:0012552, MedGen:C1970712, OMIM:610755, Orphanet:276152
ClinVar preferred disease name Neoplasm|Medullary thyroid carcinoma|Hereditary cancer-predisposing syndrome|not provided|Multiple endocrine neoplasia, type 2|Hepatocellular carcinoma|Multiple endocrine neoplasia, type 1|Multiple endocrine neoplasia, type 2a|Multiple endocrine neoplasia, type 2b|Familial medullary thyroid carcinoma|Multiple endocrine neoplasia type 4
HGVS variant names NC 000010.10:g.43613840G>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:CA008641|OMIM:164761.0027|UniProtKB:P07949#VAR 006335
Gene symbol:Gene id. RET:5979
Molecular consequence SO:0001583|missense variant
Allele origin
dbSNP ID 78014899
Variant Flags
:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV000032037; RCV000410061; RCV000411546; RCV002307370; RCV002426530;
Chromosome 10:43613840..43613840
ClinVar Allele ID 47215
Disease database name and identifier MONDO:MONDO:0015356, MeSH:D009386, MedGen:C0027672, Orphanet:140162|MONDO:MONDO:0019003, MedGen:C4048306, Orphanet:653|MedGen:CN311636|MONDO:MONDO:0008234, MeSH:D018813, MedGen:C0025268, OMIM:171400, Orphanet:247698, Orphanet:653|MONDO:MONDO:0008082, MeSH:D018814, MedGen:C0025269, OMIM:162300, Orphanet:247709, Orphanet:653
ClinVar preferred disease name Hereditary cancer-predisposing syndrome|Multiple endocrine neoplasia, type 2|MEN2 phenotype: Unclassified|Multiple endocrine neoplasia, type 2a|Multiple endocrine neoplasia, type 2b
HGVS variant names NC 000010.10:g.43613840G>T
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:CA008648|UniProtKB:P07949#VAR 006335
Gene symbol:Gene id. RET:5979
Molecular consequence SO:0001583|missense variant
Allele origin germline
dbSNP ID 78014899
Variant Flags
:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV003316935;
Chromosome 10:43613840..43613843
ClinVar Allele ID 2738194
Disease database name and identifier MONDO:MONDO:0008234, MeSH:D018813, MedGen:C0025268, OMIM:171400, Orphanet:247698, Orphanet:653
ClinVar preferred disease name Multiple endocrine neoplasia, type 2a
HGVS variant names NC 000010.10:g.43613840 43613843delinsCCTT
ClinVar review status criteria provided, single submitter
Clinical Significance Pathogenic
Variant type Indel
Sequence Ontology for variant type SO:1000032
Gene symbol:Gene id. RET:5979
Molecular consequence SO:0001583|missense variant
Allele origin unknown
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