ClinVar Genomic variation as it relates to human health
NM_020975.6(RET):c.2508C>T (p.Ser836=)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
-
NM_020975.6(RET):c.2508C>T (p.Ser836=)
Variation ID: 24946 Accession: VCV000024946.47
- Type and length
-
single nucleotide variant, 1 bp
- Location
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Cytogenetic: 10q11.21 10: 43119646 (GRCh38) [ NCBI UCSC ] 10: 43615094 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
-
First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Dec 27, 2015 Sep 29, 2024 Feb 1, 2024 - HGVS
-
Nucleotide Protein Molecular
consequenceNM_020975.6:c.2508C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_066124.1:p.Ser836= synonymous NM_000323.2:c.2508C>T NP_000314.1:p.Ser836= synonymous NM_001355216.2:c.1746C>T NP_001342145.1:p.Ser582= synonymous NM_001406743.1:c.2508C>T NP_001393672.1:p.Ser836= synonymous NM_001406744.1:c.2508C>T NP_001393673.1:p.Ser836= synonymous NM_001406759.1:c.2508C>T NP_001393688.1:p.Ser836= synonymous NM_001406760.1:c.2508C>T NP_001393689.1:p.Ser836= synonymous NM_001406761.1:c.2379C>T NP_001393690.1:p.Ser793= synonymous NM_001406762.1:c.2379C>T NP_001393691.1:p.Ser793= synonymous NM_001406763.1:c.2373C>T NP_001393692.1:p.Ser791= synonymous NM_001406764.1:c.2379C>T NP_001393693.1:p.Ser793= synonymous NM_001406765.1:c.2373C>T NP_001393694.1:p.Ser791= synonymous NM_001406766.1:c.2220C>T NP_001393695.1:p.Ser740= synonymous NM_001406767.1:c.2220C>T NP_001393696.1:p.Ser740= synonymous NM_001406768.1:c.2244C>T NP_001393697.1:p.Ser748= synonymous NM_001406769.1:c.2112C>T NP_001393698.1:p.Ser704= synonymous NM_001406770.1:c.2220C>T NP_001393699.1:p.Ser740= synonymous NM_001406771.1:c.2070C>T NP_001393700.1:p.Ser690= synonymous NM_001406772.1:c.2112C>T NP_001393701.1:p.Ser704= synonymous NM_001406773.1:c.2070C>T NP_001393702.1:p.Ser690= synonymous NM_001406774.1:c.1983C>T NP_001393703.1:p.Ser661= synonymous NM_001406775.1:c.1782C>T NP_001393704.1:p.Ser594= synonymous NM_001406776.1:c.1782C>T NP_001393705.1:p.Ser594= synonymous NM_001406777.1:c.1782C>T NP_001393706.1:p.Ser594= synonymous NM_001406778.1:c.1782C>T NP_001393707.1:p.Ser594= synonymous NM_001406779.1:c.1611C>T NP_001393708.1:p.Ser537= synonymous NM_001406780.1:c.1611C>T NP_001393709.1:p.Ser537= synonymous NM_001406781.1:c.1611C>T NP_001393710.1:p.Ser537= synonymous NM_001406782.1:c.1611C>T NP_001393711.1:p.Ser537= synonymous NM_001406783.1:c.1482C>T NP_001393712.1:p.Ser494= synonymous NM_001406784.1:c.1518C>T NP_001393713.1:p.Ser506= synonymous NM_001406785.1:c.1491C>T NP_001393714.1:p.Ser497= synonymous NM_001406786.1:c.1482C>T NP_001393715.1:p.Ser494= synonymous NM_001406787.1:c.1476C>T NP_001393716.1:p.Ser492= synonymous NM_001406788.1:c.1323C>T NP_001393717.1:p.Ser441= synonymous NM_001406789.1:c.1323C>T NP_001393718.1:p.Ser441= synonymous NM_001406790.1:c.1323C>T NP_001393719.1:p.Ser441= synonymous NM_001406791.1:c.1203C>T NP_001393720.1:p.Ser401= synonymous NM_001406792.1:c.1059C>T NP_001393721.1:p.Ser353= synonymous NM_001406793.1:c.1059C>T NP_001393722.1:p.Ser353= synonymous NM_001406794.1:c.1059C>T NP_001393723.1:p.Ser353= synonymous NM_020629.2:c.2508C>T NP_065680.1:p.Ser836= synonymous NM_020630.7:c.2508C>T NP_065681.1:p.Ser836= synonymous NC_000010.11:g.43119646C>T NC_000010.10:g.43615094C>T NG_007489.1:g.47578C>T LRG_518:g.47578C>T LRG_518t1:c.2508C>T LRG_518p1:p.Ser836= LRG_518t2:c.2508C>T LRG_518p2:p.Ser836= - Protein change
- -
- Other names
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p.S836S:AGC>AGT
- Canonical SPDI
- NC_000010.11:43119645:C:T
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
- -
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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0.03594 (T)
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
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1000 Genomes Project 0.03594
1000 Genomes Project 30x 0.03607
The Genome Aggregation Database (gnomAD) 0.03791
Trans-Omics for Precision Medicine (TOPMed) 0.03807
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.04245
The Genome Aggregation Database (gnomAD), exomes 0.04495
Exome Aggregation Consortium (ExAC) 0.04666
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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RET | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
3595 | 3717 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Benign/Likely benign (2) |
criteria provided, multiple submitters, no conflicts
|
Apr 27, 2017 | RCV000203081.15 | |
Likely benign (1) |
criteria provided, single submitter
|
Apr 27, 2017 | RCV000359214.13 | |
Likely benign (1) |
criteria provided, single submitter
|
Apr 27, 2017 | RCV000327711.13 | |
Benign (10) |
criteria provided, multiple submitters, no conflicts
|
Aug 15, 2023 | RCV000151741.38 | |
Likely benign (1) |
criteria provided, single submitter
|
Apr 27, 2017 | RCV000264509.13 | |
Benign/Likely benign (3) |
criteria provided, multiple submitters, no conflicts
|
Dec 18, 2020 | RCV000712296.21 | |
Benign (1) |
criteria provided, single submitter
|
May 7, 2019 | RCV001015789.11 | |
Benign (2) |
criteria provided, multiple submitters, no conflicts
|
Feb 1, 2024 | RCV001080523.15 | |
Benign (1) |
criteria provided, single submitter
|
Jul 7, 2023 | RCV003315509.8 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
|
---|---|---|---|---|---|
Benign
(Feb 19, 2015)
|
criteria provided, single submitter
Method: clinical testing
|
Multiple endocrine neoplasia
Affected status: unknown
Allele origin:
unknown
|
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia
Accession: SCV000258171.2
First in ClinVar: Dec 27, 2015 Last updated: Dec 27, 2015 |
|
|
Benign
(Oct 31, 2016)
|
criteria provided, single submitter
Method: clinical testing
|
not specified
Affected status: yes
Allele origin:
germline
|
GeneDx
Accession: SCV000171360.6
First in ClinVar: Jun 23, 2014 Last updated: Sep 28, 2017 |
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. (less)
|
|
Benign
(May 11, 2018)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
germline
|
Athena Diagnostics
Accession: SCV000842756.1
First in ClinVar: Oct 20, 2018 Last updated: Oct 20, 2018 |
|
|
Benign
(May 06, 2015)
|
criteria provided, single submitter
Method: clinical testing
|
not specified
Affected status: unknown
Allele origin:
germline
|
Eurofins Ntd Llc (ga)
Accession: SCV000226158.5
First in ClinVar: Jun 28, 2015 Last updated: Sep 28, 2017 |
Number of individuals with the variant: 6
Sex: mixed
|
|
Benign
(Feb 06, 2014)
|
criteria provided, single submitter
Method: clinical testing
|
not specified
Affected status: not provided
Allele origin:
germline
|
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Accession: SCV000200118.5
First in ClinVar: Jan 30, 2015 Last updated: Sep 28, 2017 |
Number of individuals with the variant: 8
|
|
Benign
(Dec 18, 2020)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
germline
|
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV000605018.5
First in ClinVar: Feb 17, 2019 Last updated: Jan 08, 2022 |
|
|
Benign
(Jul 07, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
Multiple endocrine neoplasia type 2B
Affected status: yes
Allele origin:
germline
|
KCCC/NGS Laboratory, Kuwait Cancer Control Center
Accession: SCV004017338.1
First in ClinVar: Jul 29, 2023 Last updated: Jul 29, 2023 |
|
|
Benign
(Aug 15, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
not specified
Affected status: unknown
Allele origin:
germline
|
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital
Accession: SCV002550389.4
First in ClinVar: Jul 30, 2022 Last updated: Aug 18, 2023 |
|
|
Benign
(Mar 28, 2019)
|
criteria provided, single submitter
Method: clinical testing
|
Multiple endocrine neoplasia, type 2
Affected status: unknown
Allele origin:
germline
|
Color Diagnostics, LLC DBA Color Health
Accession: SCV004357251.1
First in ClinVar: Feb 14, 2024 Last updated: Feb 14, 2024 |
|
|
Benign
(Feb 01, 2024)
|
criteria provided, single submitter
Method: clinical testing
|
Multiple endocrine neoplasia, type 2
Affected status: unknown
Allele origin:
germline
|
Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000556205.8
First in ClinVar: Apr 17, 2017 Last updated: Feb 28, 2024 |
|
|
Benign
(May 07, 2019)
|
criteria provided, single submitter
Method: clinical testing
|
Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
|
Ambry Genetics
Accession: SCV001176664.4
First in ClinVar: Mar 16, 2020 Last updated: May 01, 2024 |
Comment:
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation … (more)
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. (less)
|
|
Likely benign
(-)
|
criteria provided, single submitter
Method: not provided
|
not provided
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
germline
|
Breakthrough Genomics, Breakthrough Genomics
Accession: SCV005220646.1
First in ClinVar: Sep 29, 2024 Last updated: Sep 29, 2024 |
|
|
Benign
(-)
|
criteria provided, single submitter
Method: clinical testing
|
NOT SPECIFIED
Affected status: unknown
Allele origin:
germline
|
PreventionGenetics, part of Exact Sciences
Accession: SCV000313720.1
First in ClinVar: Oct 02, 2016 Last updated: Oct 02, 2016 |
|
|
Likely benign
(Apr 27, 2017)
|
criteria provided, single submitter
Method: clinical testing
|
Multiple endocrine neoplasia
Affected status: unknown
Allele origin:
germline
|
Illumina Laboratory Services, Illumina
Accession: SCV000362359.3
First in ClinVar: Dec 06, 2016 Last updated: May 31, 2020 |
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. (less)
|
|
Likely benign
(Apr 27, 2017)
|
criteria provided, single submitter
Method: clinical testing
|
Renal hypodysplasia/aplasia 1
Affected status: unknown
Allele origin:
germline
|
Illumina Laboratory Services, Illumina
Accession: SCV000362357.3
First in ClinVar: Dec 06, 2016 Last updated: May 31, 2020 |
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. (less)
|
|
Likely benign
(Apr 27, 2017)
|
criteria provided, single submitter
Method: clinical testing
|
Hirschsprung disease, susceptibility to, 1
Affected status: unknown
Allele origin:
germline
|
Illumina Laboratory Services, Illumina
Accession: SCV000362358.3
First in ClinVar: Dec 06, 2016 Last updated: May 31, 2020 |
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. (less)
|
|
Likely benign
(Apr 27, 2017)
|
criteria provided, single submitter
Method: clinical testing
|
Pheochromocytoma
Affected status: unknown
Allele origin:
germline
|
Illumina Laboratory Services, Illumina
Accession: SCV000362356.3
First in ClinVar: Dec 06, 2016 Last updated: May 31, 2020 |
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. (less)
|
|
Benign
(-)
|
no assertion criteria provided
Method: clinical testing
|
not specified
Affected status: yes
Allele origin:
germline
|
Genome Diagnostics Laboratory, University Medical Center Utrecht
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001929156.1 First in ClinVar: Sep 24, 2021 Last updated: Sep 24, 2021 |
|
|
Benign
(-)
|
no assertion criteria provided
Method: clinical testing
|
not specified
Affected status: yes
Allele origin:
germline
|
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001956942.1 First in ClinVar: Oct 02, 2021 Last updated: Oct 02, 2021 |
|
|
Benign
(-)
|
no assertion criteria provided
Method: clinical testing
|
not specified
Affected status: yes
Allele origin:
germline
|
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001966148.1 First in ClinVar: Oct 07, 2021 Last updated: Oct 07, 2021 |
|
|
Benign
(-)
|
no assertion criteria provided
Method: clinical testing
|
not specified
Affected status: yes
Allele origin:
germline
|
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)
Study: VKGL Data-share Consensus
Accession: SCV001800763.1 First in ClinVar: Aug 21, 2021 Last updated: Aug 21, 2021 |
|
|
Benign
(-)
|
no assertion criteria provided
Method: clinical testing
|
not specified
Affected status: yes
Allele origin:
germline
|
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001741928.3 First in ClinVar: Jul 07, 2021 Last updated: Sep 08, 2021 |
|
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
---|---|---|---|---|
Induction of RET dependent and independent pro-inflammatory programs in human peripheral blood mononuclear cells from Hirschsprung patients. | Rusmini M | PloS one | 2013 | PMID: 23527089 |
Medullary thyroid carcinoma (MTC) and RET proto-oncogene: mutation spectrum in the familial cases and a meta-analysis of studies on the sporadic form. | Figlioli G | Mutation research | 2013 | PMID: 23059849 |
Clinical relevance of RET variants G691S, L769L, S836S and S904S to sporadic medullary thyroid cancer. | Machens A | Clinical endocrinology | 2012 | PMID: 22111543 |
The RET polymorphic allele S836S is associated with early metastatic disease in patients with hereditary or sporadic medullary thyroid carcinoma. | Siqueira DR | Endocrine-related cancer | 2010 | PMID: 20801952 |
Polymorphisms in exon 13 and intron 14 of the RET protooncogene: genetic modifiers of medullary thyroid carcinoma? | Baumgartner-Parzer SM | The Journal of clinical endocrinology and metabolism | 2005 | PMID: 16118333 |
RET polymorphisms and haplotypes and risk of differentiated thyroid cancer. | Ho T | The Laryngoscope | 2005 | PMID: 15933516 |
A rare haplotype of the RET proto-oncogene is a risk-modifying allele in hirschsprung disease. | Griseri P | American journal of human genetics | 2002 | PMID: 12214285 |
Germline sequence variant S836S in the RET proto-oncogene is associated with low level predisposition to sporadic medullary thyroid carcinoma in the Spanish population. | Ruiz A | Clinical endocrinology | 2001 | PMID: 11589684 |
A single-nucleotide polymorphic variant of the RET proto-oncogene is underrepresented in sporadic Hirschsprung disease. | Griseri P | European journal of human genetics : EJHG | 2000 | PMID: 10980580 |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=RET | - | - | - | - |
Text-mined citations for rs1800862 ...
HelpRecord last updated Nov 10, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.