ClinVar Genomic variation as it relates to human health
NM_001048174.2(MUTYH):c.1347G>C (p.Thr449=)
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
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NM_001048174.2(MUTYH):c.1347G>C (p.Thr449=)
Variation ID: 183787 Accession: VCV000183787.76
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 1p34.1 1: 45331227 (GRCh38) [ NCBI UCSC ] 1: 45796899 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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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 Jun 28, 2015 Oct 20, 2024 Aug 1, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001048174.2:c.1347G>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001041639.1:p.Thr449= synonymous NM_001128425.2:c.1431G>C MANE Plus Clinical Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001121897.1:p.Thr477= synonymous NM_001048171.2:c.1347G>C NP_001041636.2:p.Thr449= synonymous NM_001048172.2:c.1350G>C NP_001041637.1:p.Thr450= synonymous NM_001048173.2:c.1347G>C NP_001041638.1:p.Thr449= synonymous NM_001293190.2:c.1392G>C NP_001280119.1:p.Thr464= synonymous NM_001293191.2:c.1380G>C NP_001280120.1:p.Thr460= synonymous NM_001293192.2:c.1071G>C NP_001280121.1:p.Thr357= synonymous NM_001293195.2:c.1347G>C NP_001280124.1:p.Thr449= synonymous NM_001293196.2:c.1071G>C NP_001280125.1:p.Thr357= synonymous NM_001350650.2:c.1002G>C NP_001337579.1:p.Thr334= synonymous NM_001350651.2:c.1002G>C NP_001337580.1:p.Thr334= synonymous NM_012222.3:c.1422G>C NP_036354.1:p.Thr474= synonymous NR_146882.2:n.1575G>C non-coding transcript variant NR_146883.2:n.1424G>C non-coding transcript variant NC_000001.11:g.45331227C>G NC_000001.10:g.45796899C>G NG_008189.1:g.14244G>C LRG_220:g.14244G>C LRG_220t1:c.1431G>C LRG_220p1:p.Thr477= - Protein change
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- Other names
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- Canonical SPDI
- NC_000001.11:45331226:C:G
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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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0.01038 (G)
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
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NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00415
The Genome Aggregation Database (gnomAD), exomes 0.00461
Exome Aggregation Consortium (ExAC) 0.00488
Trans-Omics for Precision Medicine (TOPMed) 0.00560
The Genome Aggregation Database (gnomAD) 0.00596
1000 Genomes Project 30x 0.00968
1000 Genomes Project 0.01038
- 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
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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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MUTYH | - | - |
GRCh38 GRCh37 |
2689 | 2845 |
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 (5) |
criteria provided, multiple submitters, no conflicts
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Apr 11, 2023 | RCV000162570.17 | |
Benign (7) |
criteria provided, multiple submitters, no conflicts
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Aug 15, 2023 | RCV000174706.33 | |
Benign/Likely benign (7) |
criteria provided, multiple submitters, no conflicts
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Aug 1, 2024 | RCV000759880.47 | |
Benign/Likely benign (2) |
criteria provided, multiple submitters, no conflicts
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Feb 1, 2024 | RCV001083142.20 | |
Uncertain significance (1) |
no assertion criteria provided
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- | RCV001353747.10 | |
Benign (1) |
criteria provided, single submitter
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Mar 17, 2022 | RCV002498804.8 |
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. |
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Benign
(Mar 29, 2016)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
germline
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Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Accession: SCV000539813.1
First in ClinVar: Jun 28, 2015 Last updated: Jun 28, 2015 |
Comment:
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or … (more)
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Silent, high frequency (less)
Method: Genome/Exome Filtration
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Benign
(Mar 21, 2016)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
germline
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PreventionGenetics, part of Exact Sciences
Accession: SCV000806343.1
First in ClinVar: Sep 13, 2018 Last updated: Sep 13, 2018 |
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Benign
(Aug 21, 2014)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
germline
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Eurofins Ntd Llc (ga)
Accession: SCV000226060.5
First in ClinVar: Jun 28, 2015 Last updated: Sep 13, 2018 |
Number of individuals with the variant: 1
Sex: mixed
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Likely benign
(Feb 09, 2018)
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criteria provided, single submitter
Method: clinical testing
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Familial adenomatous polyposis 2
Affected status: unknown
Allele origin:
germline
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Illumina Laboratory Services, Illumina
Accession: SCV001253573.1
First in ClinVar: May 31, 2020 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). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. (less)
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Benign
(Aug 18, 2020)
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criteria provided, single submitter
Method: curation
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Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
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Sema4, Sema4
Accession: SCV002532237.1
First in ClinVar: Jun 24, 2022 Last updated: Jun 24, 2022 |
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Benign
(Apr 28, 2023)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV001159237.6
First in ClinVar: Feb 10, 2020 Last updated: Feb 20, 2024 |
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Benign
(Aug 01, 2024)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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CeGaT Center for Human Genetics Tuebingen
Accession: SCV001248076.26
First in ClinVar: May 12, 2020 Last updated: Oct 20, 2024 |
Comment:
MUTYH: BP4, BP7, BS1, BS2
Number of individuals with the variant: 15
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Benign
(Mar 03, 2015)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV001836968.1
First in ClinVar: Sep 10, 2021 Last updated: Sep 10, 2021 |
Comment:
This variant is associated with the following publications: (PMID: 27829682, 27884173, 16774938, 20981092)
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Benign
(Mar 21, 2016)
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criteria provided, single submitter
Method: clinical testing
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Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
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Color Diagnostics, LLC DBA Color Health
Accession: SCV000685576.2
First in ClinVar: Feb 19, 2018 Last updated: Dec 11, 2022 |
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Benign
(Aug 31, 2020)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
unknown
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Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV000889520.4
First in ClinVar: Mar 14, 2019 Last updated: Dec 31, 2022 |
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Benign
(Mar 17, 2022)
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criteria provided, single submitter
Method: clinical testing
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Familial adenomatous polyposis 2
Gastric cancer
Affected status: unknown
Allele origin:
unknown
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Fulgent Genetics, Fulgent Genetics
Accession: SCV002795890.1
First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022 |
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Benign
(Apr 11, 2023)
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criteria provided, single submitter
Method: clinical testing
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Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
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Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C.
Accession: SCV004014952.1
First in ClinVar: Jul 22, 2023 Last updated: Jul 22, 2023 |
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Benign
(Aug 15, 2023)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
germline
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Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital
Accession: SCV002547277.4
First in ClinVar: Jul 17, 2022 Last updated: Aug 18, 2023 |
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Benign
(Feb 01, 2024)
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criteria provided, single submitter
Method: clinical testing
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Familial adenomatous polyposis 2
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000557584.9
First in ClinVar: Apr 17, 2017 Last updated: Feb 20, 2024 |
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Benign
(Dec 17, 2014)
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criteria provided, single submitter
Method: clinical testing
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Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV000212986.9
First in ClinVar: Mar 24, 2015 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)
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Likely benign
(-)
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criteria provided, single submitter
Method: not provided
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not provided
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
germline
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Breakthrough Genomics, Breakthrough Genomics
Accession: SCV005262071.1
First in ClinVar: Sep 29, 2024 Last updated: Sep 29, 2024 |
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Likely benign
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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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: SCV001960022.1 First in ClinVar: Oct 02, 2021 Last updated: Oct 02, 2021 |
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Likely benign
(Jun 21, 2017)
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no assertion criteria provided
Method: clinical testing
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Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
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True Health Diagnostics
Accession: SCV000788064.1
First in ClinVar: Feb 19, 2018 Last updated: Feb 19, 2018 |
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Uncertain significance
(-)
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no assertion criteria provided
Method: clinical testing
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Carcinoma of colon
Affected status: yes
Allele origin:
unknown
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Department of Pathology and Laboratory Medicine, Sinai Health System
Additional submitter:
Franklin by Genoox
Study: The Canadian Open Genetics Repository (COGR)
Accession: SCV000592717.2 First in ClinVar: Jun 28, 2015 Last updated: Apr 13, 2021 |
Comment:
The p.Thr477Thr (c.1431G>C ) variant (alias 1389G>C) has been previously reported in the literature in 14/332 proband chromosomes (frequency 0.048) in individuals affected with either … (more)
The p.Thr477Thr (c.1431G>C ) variant (alias 1389G>C) has been previously reported in the literature in 14/332 proband chromosomes (frequency 0.048) in individuals affected with either adenomatous polyposis, gastric cancer or colorectal cancer, however controls were not included in these studies (Peterlongo 2006, Tao 2004, Yanaru-Fujisawa 2008). This variant has also been identified in the HGMD and LOVD databases, however it is not expected to have clinical significance because it does not alter an amino acid residue, is not located near a splice junction, and has been reported in dbSNP (ID#:rs74318065), by the 1000 genomes project (frequency 0.016), and ESP project (frequency 0.004). However, there is some conflicting information in the literature. In one study the variant c.1431G > C was found to be in complete linkage disequilibrium with two other MUTYH variants, –280G > A and c.36+11C>T (alias IVS1+11C>T). A statistically significant association was demonstrated between one of these variants, c.36+11C>T and increased CRC risk (Tao 2008). This indicates that individuals with the MUTYH – 280A/c.36+11T/c.1431C genotypes may be susceptible to CRC (Tao 2008). However, replication in additional cohorts and additional functional evidence would be required to validate this finding. In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time. Therefore, this variant is classified as a variant of unknown significance (VUS). (less)
Number of individuals with the variant: 3
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Likely benign
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)
Study: VKGL Data-share Consensus
Accession: SCV001800318.1 First in ClinVar: Aug 21, 2021 Last updated: Aug 21, 2021 |
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Benign
(-)
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no assertion criteria provided
Method: clinical testing
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not specified
Affected status: yes
Allele origin:
germline
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Genome Diagnostics Laboratory, Amsterdam University Medical Center
Study: VKGL Data-share Consensus
Accession: SCV001807696.1 First in ClinVar: Aug 27, 2021 Last updated: Aug 27, 2021 |
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Likely benign
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Clinical Genetics, Academic Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001921567.1 First in ClinVar: Sep 24, 2021 Last updated: Sep 24, 2021 |
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Benign
(-)
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no assertion criteria provided
Method: clinical testing
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not specified
Affected status: yes
Allele origin:
germline
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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: SCV001964337.1 First in ClinVar: Oct 07, 2021 Last updated: Oct 07, 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 |
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Genomic and functional analyses of MUTYH in Japanese patients with adenomatous polyposis. | Yanaru-Fujisawa R | Clinical genetics | 2008 | PMID: 18422726 |
Association between genetic polymorphisms of the base excision repair gene MUTYH and increased colorectal cancer risk in a Japanese population. | Tao H | Cancer science | 2008 | PMID: 18271935 |
Similar colorectal cancer risk in patients with monoallelic and biallelic mutations in the MYH gene identified in a population with adenomatous polyposis. | Olschwang S | Genetic testing | 2007 | PMID: 17949294 |
Increased frequency of disease-causing MYH mutations in colon cancer families. | Peterlongo P | Carcinogenesis | 2006 | PMID: 16774938 |
Germline mutations in the MYH gene in Swedish familial and sporadic colorectal cancer. | Zhou XL | Genetic testing | 2005 | PMID: 15943555 |
Comprehensive analysis of the contribution of germline MYH variation to early-onset colorectal cancer. | Fleischmann C | International journal of cancer | 2004 | PMID: 14991577 |
Somatic mutations and single nucleotide polymorphisms of base excision repair genes involved in the repair of 8-hydroxyguanine in damaged DNA. | Shinmura K | Cancer letters | 2001 | PMID: 11295288 |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=MUTYH | - | - | - | - |
Text-mined citations for rs74318065 ...
HelpRecord last updated Nov 25, 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.