ClinVar Genomic variation as it relates to human health
NM_002693.3(POLG):c.3428A>G (p.Glu1143Gly)
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_002693.3(POLG):c.3428A>G (p.Glu1143Gly)
Variation ID: 21312 Accession: VCV000021312.51
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 15q26.1 15: 89318595 (GRCh38) [ NCBI UCSC ] 15: 89861826 (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 Apr 4, 2013 Feb 20, 2024 May 6, 2021 - HGVS
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Nucleotide Protein Molecular
consequenceNM_002693.3(POLG):c.3428A>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NM_002693.3:c.3428A>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_002684.1:p.Glu1143Gly missense NM_001126131.2:c.3428A>G NP_001119603.1:p.Glu1143Gly missense NC_000015.10:g.89318595T>C NC_000015.9:g.89861826T>C NG_008218.2:g.21201A>G NG_011736.1:g.79633T>C LRG_500:g.79633T>C LRG_765:g.21201A>G LRG_765t1:c.3428A>G LRG_765p1:p.Glu1143Gly P54098:p.Glu1143Gly - Protein change
- E1143G
- Other names
- -
- Canonical SPDI
- NC_000015.10:89318594:T:C
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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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0.01138 (C)
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
1000 Genomes Project 30x 0.00984
Trans-Omics for Precision Medicine (TOPMed) 0.02426
Exome Aggregation Consortium (ExAC) 0.02813
The Genome Aggregation Database (gnomAD), exomes 0.02873
The Genome Aggregation Database (gnomAD) 0.02704
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.02754
1000 Genomes Project 0.01138
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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FANCI | - | - |
GRCh38 GRCh37 |
1948 | 2141 | |
POLG | - | - |
GRCh38 GRCh37 |
1 | 2958 | |
POLGARF | - | - | GRCh38 | - | 2914 |
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 (1) |
reviewed by expert panel
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May 6, 2021 | RCV000020476.12 | |
Benign/Likely benign (9) |
criteria provided, multiple submitters, no conflicts
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Nov 29, 2022 | RCV000118018.34 | |
Likely benign (1) |
criteria provided, single submitter
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Jun 14, 2016 | RCV000386578.13 | |
Benign (2) |
criteria provided, multiple submitters, no conflicts
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Feb 1, 2024 | RCV000469563.17 | |
Benign (6) |
criteria provided, multiple submitters, no conflicts
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Nov 29, 2023 | RCV000676317.26 | |
Benign (1) |
criteria provided, single submitter
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Aug 3, 2021 | RCV000755650.11 | |
not provided (1) |
no classification provided
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- | RCV000999632.9 | |
Likely benign (1) |
criteria provided, single submitter
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Apr 27, 2017 | RCV001119316.12 | |
Benign (1) |
criteria provided, single submitter
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Aug 29, 2021 | RCV001847611.11 | |
Benign (1) |
criteria provided, single submitter
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Mar 21, 2016 | RCV002311518.8 |
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
(May 06, 2021)
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reviewed by expert panel
Method: curation
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Mitochondrial disease
(Autosomal recessive inheritance)
Affected status: unknown
Allele origin:
germline
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ClinGen Mitochondrial Disease Nuclear and Mitochondrial Variant Curation Expert Panel, ClinGen
Accession: SCV001736741.1
First in ClinVar: Jun 19, 2021 Last updated: Jun 19, 2021 |
Comment:
The c.3428A>G (p.E1143G) variant in POLG has been reported 2.881 % in gnomAD (BA1). It is also seen in the homozygous state in 175 individuals … (more)
The c.3428A>G (p.E1143G) variant in POLG has been reported 2.881 % in gnomAD (BA1). It is also seen in the homozygous state in 175 individuals in gnomAD and 65 in ExAC (BS2). In summary, this variant meets criteria to be classified as benign for primary mitochondrial disease inherited in a recessive manner. ntDNA Mitochondrial ACMG-AMP Criteria for POLG applied: BA1 & BS2. (less)
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Benign
(-)
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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: SCV000309143.1
First in ClinVar: Oct 02, 2016 Last updated: Oct 02, 2016 |
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Likely benign
(Jun 14, 2016)
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criteria provided, single submitter
Method: clinical testing
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Fanconi Anemia
Affected status: unknown
Allele origin:
germline
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Illumina Laboratory Services, Illumina
Accession: SCV000483523.2
First in ClinVar: Dec 06, 2016 Last updated: Dec 06, 2016 |
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Benign
(Jul 26, 2018)
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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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Athena Diagnostics Inc
Accession: SCV000843333.1
First in ClinVar: Aug 05, 2018 Last updated: Aug 05, 2018 |
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Likely benign
(Apr 27, 2017)
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criteria provided, single submitter
Method: clinical testing
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POLG-Related Spectrum Disorders
Affected status: unknown
Allele origin:
germline
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Illumina Laboratory Services, Illumina
Accession: SCV001277698.1
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). 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)
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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: SCV001936001.1
First in ClinVar: Sep 26, 2021 Last updated: Sep 26, 2021 |
Comment:
This variant is associated with the following publications: (PMID: 17980715, 21686371, 25497598, 23448099, 17088268, 22166854, 23783014, 20691285, 20981092, 21228398, 15477547, 27884173, 26104464, 26468652, 18991199, 24122062, … (more)
This variant is associated with the following publications: (PMID: 17980715, 21686371, 25497598, 23448099, 17088268, 22166854, 23783014, 20691285, 20981092, 21228398, 15477547, 27884173, 26104464, 26468652, 18991199, 24122062, 30255931, 25925909, 25462018, 33469851) (less)
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Benign
(Aug 29, 2021)
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criteria provided, single submitter
Method: clinical testing
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Hereditary spastic paraplegia
Affected status: yes
Allele origin:
germline
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Genome Diagnostics Laboratory, The Hospital for Sick Children
Accession: SCV002105584.1
First in ClinVar: Mar 19, 2022 Last updated: Mar 19, 2022 |
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Benign
(Nov 29, 2022)
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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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Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV002766201.1
First in ClinVar: Dec 24, 2022 Last updated: Dec 24, 2022 |
Comment:
Variant summary: POLG c.3428A>G (p.Glu1143Gly) results in a non-conservative amino acid change located in the palm domain (IPR001098) of the encoded protein sequence. Five of … (more)
Variant summary: POLG c.3428A>G (p.Glu1143Gly) results in a non-conservative amino acid change located in the palm domain (IPR001098) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.029 in 251414 control chromosomes in the gnomAD database, including 156 homozygotes, strongly suggesting that the variant is benign. c.3428A>G has been reported in the literature in cis with a pathogenic variant in individuals affected with POLG-Related Spectrum Disorders, indicating that it is likely benign and not the cause of the disease phenotype (e.g. Ferrari_2005, Horvath_2006). At least one publication reports experimental evidence evaluating an impact on protein function and the results showed no damaging effect of this variant on polymerase activity (e.g. Chan_2006). Thirteen submitters have provided clinical-significance assessments for this variant to ClinVar after 2014. All classified the variant as either benign (n= 9) or likely benign (n=4). Based on the evidence outlined above, the variant was classified as benign. (less)
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Benign
(Aug 03, 2021)
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criteria provided, single submitter
Method: clinical testing
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Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 1
Progressive sclerosing poliodystrophy Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1 Mitochondrial DNA depletion syndrome 1 Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis Mitochondrial DNA depletion syndrome 4b
Affected status: unknown
Allele origin:
unknown
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Fulgent Genetics, Fulgent Genetics
Accession: SCV000883049.2
First in ClinVar: Feb 18, 2019 Last updated: Dec 31, 2022 |
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Benign
(Feb 01, 2024)
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criteria provided, single submitter
Method: clinical testing
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Progressive sclerosing poliodystrophy
Affected status: unknown
Allele origin:
germline
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Invitae
Accession: SCV000556246.7
First in ClinVar: Apr 17, 2017 Last updated: Feb 14, 2024 |
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Benign
(Nov 29, 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: SCV000604901.7
First in ClinVar: Oct 02, 2016 Last updated: Feb 20, 2024 |
|
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Benign
(Apr 17, 2015)
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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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Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia
Accession: SCV000257929.2
First in ClinVar: Jun 28, 2015 Last updated: Jun 28, 2015 |
|
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Likely benign
(Mar 28, 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: SCV000540098.1
First in ClinVar: Oct 02, 2016 Last updated: Oct 02, 2016 |
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: Frequency in 1000Genomes: 37/2178=1.6% (less)
Method: Genome/Exome Filtration
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Benign
(Mar 14, 2014)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
germline
|
Eurofins Ntd Llc (ga)
Accession: SCV000203322.7
First in ClinVar: Jan 29, 2015 Last updated: May 03, 2018 |
Number of individuals with the variant: 3
Sex: mixed
|
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Benign
(Oct 01, 2018)
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criteria provided, single submitter
Method: clinical testing
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Progressive sclerosing poliodystrophy
Affected status: unknown
Allele origin:
germline
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Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine
Accession: SCV000887280.1
First in ClinVar: Dec 26, 2017 Last updated: Dec 26, 2017 |
Comment:
The NM_002693.2:c.3428A>G (NP_002684.1:p.Glu1143Gly) [GRCH38: NC_000015.10:g.89318595T>C] variant in POLG gene is interpretated to be a Benign based on ACMG guidelines (PMID: 25741868). This variant meets the … (more)
The NM_002693.2:c.3428A>G (NP_002684.1:p.Glu1143Gly) [GRCH38: NC_000015.10:g.89318595T>C] variant in POLG gene is interpretated to be a Benign based on ACMG guidelines (PMID: 25741868). This variant meets the following evidence codes reported in the ACMG-guideline. BS1:The minor allele frequency of this allele is high for Mitochondrial DNA depletion syndrome 4A (Alpers type). BS2:Observation of the variant in controls is inconsistent with penetrance of Mitochondrial DNA depletion syndrome 4A (Alpers type). Based on the evidence criteria codes applied, the variant is suggested to be Benign. (less)
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Benign
(Mar 21, 2016)
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criteria provided, single submitter
Method: clinical testing
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Inborn genetic diseases
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV000846384.3
First in ClinVar: Nov 08, 2018 Last updated: Nov 29, 2022 |
Comment:
This alteration is classified as benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA … (more)
This alteration is classified as benign based on a combination of the following: 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)
Number of individuals with the variant: 1
|
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Likely benign
(-)
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no assertion criteria provided
Method: clinical testing
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AllHighlyPenetrant
(Autosomal recessive inheritance)
Affected status: unknown
Allele origin:
germline
|
Genetic Services Laboratory, University of Chicago
Accession: SCV000152336.2
First in ClinVar: May 17, 2014 Last updated: Jul 06, 2014 |
Comment:
Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated … (more)
Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. (less)
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Likely benign
(Feb 25, 2016)
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no assertion criteria provided
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
unknown
|
Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV000802076.1
First in ClinVar: Aug 05, 2018 Last updated: Aug 05, 2018 |
|
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Benign
(-)
|
no assertion criteria provided
Method: clinical testing
|
not specified
Affected status: yes
Allele origin:
germline
|
Genome Diagnostics Laboratory, Amsterdam University Medical Center
Study: VKGL Data-share Consensus
Accession: SCV001807291.1 First in ClinVar: Aug 27, 2021 Last updated: Aug 27, 2021 |
|
|
Likely benign
(-)
|
no assertion criteria provided
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
|
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001743070.3 First in ClinVar: Jul 07, 2021 Last updated: Sep 08, 2021 |
|
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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: SCV001930440.1 First in ClinVar: Sep 26, 2021 Last updated: Sep 26, 2021 |
|
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Likely benign
(-)
|
no assertion criteria provided
Method: clinical testing
|
not provided
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: SCV001958733.1 First in ClinVar: Oct 02, 2021 Last updated: Oct 02, 2021 |
|
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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: SCV001968485.1 First in ClinVar: Oct 08, 2021 Last updated: Oct 08, 2021 |
|
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not provided
(-)
|
no classification provided
Method: phenotyping only
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Association with valproate-induced liver toxicity
Affected status: unknown
Allele origin:
unknown
|
GenomeConnect-Association for Creatine Deficiencies, Association for Creatine Deficiencies
Accession: SCV001156346.1
First in ClinVar: Feb 10, 2020 Last updated: Feb 10, 2020 |
Comment:
Variant interpreted as Risk factor and reported on 09-22-2017 by GTR ID 26957. Assertions are reported exactly as they appear on the patient provided laboratory … (more)
Variant interpreted as Risk factor and reported on 09-22-2017 by GTR ID 26957. Assertions are reported exactly as they appear on the patient provided laboratory report. GenomeConnect facilitates ClinVar submission from the Association for Creatine Deficiencies registry and does not attempt to reinterpret the variant. (less)
Clinical Features:
Morphological abnormality of the central nervous system (present) , Cognitive impairment (present) , Seizures (present)
Indication for testing: Diagnostic
Age: 0-9 years
Sex: male
Testing laboratory: GeneDx
Date variant was reported to submitter: 2017-09-22
Testing laboratory interpretation: risk factor
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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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The spectrum of epilepsy caused by POLG mutations. | Janssen W | Acta neurologica Belgica | 2016 | PMID: 26104464 |
Polymorphisms in DNA polymerase γ affect the mtDNA stability and the NRTI-induced mitochondrial toxicity in Saccharomyces cerevisiae. | Baruffini E | Mitochondrion | 2015 | PMID: 25462018 |
Reduced mitochondrial DNA content and heterozygous nuclear gene mutations in patients with acute liver failure. | Helbling D | Journal of pediatric gastroenterology and nutrition | 2013 | PMID: 23783014 |
Carrier testing for severe childhood recessive diseases by next-generation sequencing. | Bell CJ | Science translational medicine | 2011 | PMID: 21228398 |
POLG exon 22 skipping induced by different mechanisms in two unrelated cases of Alpers syndrome. | Mousson de Camaret B | Mitochondrion | 2011 | PMID: 20691285 |
Polymerase γ gene POLG determines the risk of sodium valproate-induced liver toxicity. | Stewart JD | Hepatology (Baltimore, Md.) | 2010 | PMID: 21038416 |
DNA polymerase gamma and mitochondrial disease: understanding the consequence of POLG mutations. | Chan SS | Biochimica et biophysica acta | 2009 | PMID: 19010300 |
Rapidly progressive neurological deterioration in a child with Alpers syndrome exhibiting a previously unremarkable brain MRI. | Brunetti-Pierri N | Neuropediatrics | 2008 | PMID: 18991199 |
1H MRS spectroscopy evidence of cerebellar high lactate in mitochondrial respiratory chain deficiency. | Boddaert N | Molecular genetics and metabolism | 2008 | PMID: 17950645 |
Mitochondrial DNA defects in Saccharomyces cerevisiae caused by functional interactions between DNA polymerase gamma mutations associated with disease in human. | Baruffini E | Biochimica et biophysica acta | 2007 | PMID: 17980715 |
The A467T and W748S POLG substitutions are a rare cause of adult-onset ataxia in Europe. | Craig K | Brain : a journal of neurology | 2007 | PMID: 17438011 |
Abundance of the POLG disease mutations in Europe, Australia, New Zealand, and the United States explained by single ancient European founders. | Hakonen AH | European journal of human genetics : EJHG | 2007 | PMID: 17426723 |
Phenotypic spectrum associated with mutations of the mitochondrial polymerase gamma gene. | Horvath R | Brain : a journal of neurology | 2006 | PMID: 16621917 |
POLG mutations in Alpers syndrome. | Nguyen KV | Neurology | 2005 | PMID: 16177225 |
Infantile hepatocerebral syndromes associated with mutations in the mitochondrial DNA polymerase-gammaA. | Ferrari G | Brain : a journal of neurology | 2005 | PMID: 15689359 |
POLG mutations in neurodegenerative disorders with ataxia but no muscle involvement. | Van Goethem G | Neurology | 2004 | PMID: 15477547 |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=POLG | - | - | - | - |
https://erepo.clinicalgenome.org/evrepo/ui/interpretation/7ab61a4c-7405-4783-9e9a-7d5720801142 | - | - | - | - |
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Text-mined citations for rs2307441 ...
HelpRecord last updated Apr 20, 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.