View genomic variant #0000000191

Chromosome	10
Allele	Unknown
Affects function (as reported)	Affects function
Affects function (by curator)	Affects function
Type	subst
DNA change (genomic) (Relative to hg19 / GRCh37)	g.43614996G>A
Published as	-
GERP	5.360
Segregation	-
DB-ID	RET_000001
MSCV	MSCV_0000191
dbSNP ID	rs79658334
Frequency	-
Sources	; clinvar;
Reference	11589684;11932300;3697657;12694233;15741265;11788682;8797874;7784092
Variant remarks	-
Genetic origin	-
Variant_disease	-
Average frequency (large NGS studies)	8.0E-5 View details
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.

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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	0000000191	+/+	c.2410G>A	p.(Val804Met)	missense_variant	-	14/19	probably_damaging(1)	r.(?)	deleterious(0.03)

Legend

ClinVar @ MSeqDR
RCVaccession	RCV000148773; RCV000182584; RCV000210181; RCV000499191; RCV000515232; RCV000586783; RCV001804750; RCV003153308; RCV003458341; RCV003460494;
Chromosome	10:43614996..43614996
ClinVar Allele ID	28984
Disease database name and identifier	.\|MONDO:MONDO:0015356, MeSH:D009386, MedGen:C0027672, Orphanet:140162\|MONDO:MONDO:0008170, MedGen:C1140680, Orphanet:213500\|MedGen:C3661900\|MONDO:MONDO:0019003, MedGen:C4048306, Orphanet:653\|MedGen:CN311636\|MONDO:MONDO:0007723, MedGen:C3888239, OMIM:142623, Orphanet:388\|MONDO:MONDO:0008234, MeSH:D018813, MedGen:C0025268, OMIM:171400, Orphanet:247698, Orphanet:653\|MONDO:MONDO:0007958, MedGen:C1833921, OMIM:155240, Orphanet:653, Orphanet:99361\|MONDO:MONDO:0024519, MedGen:C1619700, OMIM:191830, Orphanet:411709\|Human Phenotype Ontology:HP:0002666, MONDO:MONDO:0008233, MedGen:C0031511, OMIM:171300, Orphanet:29072\|MONDO:MONDO:0800031, MedGen:C1275808, OMIM:PS209880, Orphanet:661, Orphanet:99803\|MONDO:MONDO:0008082, MeSH:D018814, MedGen:C0025269, OMIM:162300, Orphanet:247709, Orphanet:653
ClinVar preferred disease name	RET-related disease\|Hereditary cancer-predisposing syndrome\|Ovarian cancer\|not provided\|Multiple endocrine neoplasia, type 2\|MEN2 phenotype: Unclassified\|Hirschsprung disease, susceptibility to, 1\|Multiple endocrine neoplasia, type 2a\|Familial medullary thyroid carcinoma\|Renal hypodysplasia/aplasia 1\|Pheochromocytoma\|Congenital central hypoventilation\|Multiple endocrine neoplasia, type 2b
HGVS variant names	NC 000010.10:g.43614996G>A
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:CA008751\|OMIM:164761.0043\|UniProtKB:P07949#VAR 006337
Gene symbol:Gene id.	RET:5979
Molecular consequence	SO:0001583\|missense variant
Allele origin
dbSNP ID	79658334
For included Variant: Tag-value pairs of disease database name and identifier, e.g. OMIM:NNNNNN	Human Phenotype Ontology:HP:0002865, MONDO:MONDO:0015277, MeSH:C536914, MedGen:C0238462, Orphanet:1332\|MONDO:MONDO:0008082, MeSH:D018814, MedGen:C0025269, OMIM:162300, Orphanet:247709, Orphanet:653
For included Variant : ClinVar preferred disease name for the concept specified by disease identifiers in CLNDISDB	Medullary thyroid carcinoma\|Multiple endocrine neoplasia, type 2b
Clinical significance for a haplotype or genotype that includes this variant. Reported as pairs of VariationID:clinical significance.	13945:Pathogenic\|618965:Pathogenic
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV000021853; RCV000419916; RCV000426266; RCV000425568; RCV000436948; RCV000437130; RCV000479688; RCV002453279; RCV003226171;
Chromosome 10:43614996..43614996
ClinVar Allele ID 47217
Disease database name and identifier 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|MedGen:CN311636|MONDO:MONDO:0019003, MedGen:C4048306, Orphanet:653|MONDO:MONDO:0007540, MeSH:D018761, MedGen:C0025267, OMIM:131100, Orphanet:652|MONDO:MONDO:0008082, MeSH:D018814, MedGen:C0025269, OMIM:162300, Orphanet:247709, Orphanet:653|MONDO:MONDO:0012552, MedGen:C1970712, OMIM:610755, Orphanet:276152|MONDO:MONDO:0008234, MeSH:D018813, MedGen:C0025268, OMIM:171400, Orphanet:247698, Orphanet:653
ClinVar preferred disease name Medullary thyroid carcinoma|Hereditary cancer-predisposing syndrome|not provided|MEN2 phenotype: Unclassified|Multiple endocrine neoplasia, type 2|Multiple endocrine neoplasia, type 1|Multiple endocrine neoplasia, type 2b|Multiple endocrine neoplasia type 4|Multiple endocrine neoplasia, type 2a
HGVS variant names NC 000010.10:g.43614996G>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:CA008758|UniProtKB:P07949#VAR 006336
Gene symbol:Gene id. RET:5979
Molecular consequence SO:0001583|missense variant
Allele origin
dbSNP ID 79658334
Variant Flags
:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV000014973; RCV000021854; RCV000354366; RCV000487450; RCV000596480; RCV000561258;
Chromosome 10:43614996..43614996
ClinVar Allele ID 28985
Disease database name and identifier MONDO:MONDO:0007958, MedGen:C1833921, OMIM:155240, Orphanet:653, Orphanet:99361|MONDO:MONDO:0017169, MedGen:C0027662, OMIM:PS131100, Orphanet:276161|MONDO:MONDO:0015356, MeSH:D009386, MedGen:C0027672, Orphanet:140162|MedGen:C3661900|MONDO:MONDO:0019003, MedGen:C4048306, Orphanet:653|MONDO:MONDO:0008234, MeSH:D018813, MedGen:C0025268, OMIM:171400, Orphanet:247698, Orphanet:653
ClinVar preferred disease name Familial medullary thyroid carcinoma|Multiple endocrine neoplasia|Hereditary cancer-predisposing syndrome|not provided|Multiple endocrine neoplasia, type 2|Multiple endocrine neoplasia, type 2a
HGVS variant names NC 000010.10:g.43614996G>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:CA008766|OMIM:164761.0044|UniProtKB:P07949#VAR 006336
Gene symbol:Gene id. RET:5979
Molecular consequence SO:0001583|missense variant
Allele origin germline
dbSNP ID 79658334
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