ClinVar Genomic variation as it relates to human health
NM_032578.4(MYPN):c.59A>G (p.Tyr20Cys)
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.
Uncertain significance(7); Likely benign(7)
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_032578.4(MYPN):c.59A>G (p.Tyr20Cys)
Variation ID: 31811 Accession: VCV000031811.45
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 10q21.3 10: 68121497 (GRCh38) [ NCBI UCSC ] 10: 69881254 (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 Apr 15, 2024 Jan 29, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_032578.4:c.59A>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_115967.2:p.Tyr20Cys missense NM_001256267.2:c.59A>G NP_001243196.1:p.Tyr20Cys missense NM_001256268.2:c.-1064A>G 5 prime UTR NR_045663.4:n.296A>G non-coding transcript variant NC_000010.11:g.68121497A>G NC_000010.10:g.69881254A>G NG_032118.1:g.20381A>G LRG_410:g.20381A>G LRG_410t1:c.59A>G LRG_410p1:p.Tyr20Cys Q86TC9:p.Tyr20Cys - Protein change
- Y20C
- Other names
- p.Y20C:TAT>TGT
- MYPN, TYR20CYS (rs140148105)
- Canonical SPDI
- NC_000010.11:68121496:A:G
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
- functional variant Sequence Ontology [SO:0001536]
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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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0.00100 (G)
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
Exome Aggregation Consortium (ExAC) 0.00092
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00092
1000 Genomes Project 30x 0.00094
The Genome Aggregation Database (gnomAD), exomes 0.00095
1000 Genomes Project 0.00100
The Genome Aggregation Database (gnomAD) 0.00130
Trans-Omics for Precision Medicine (TOPMed) 0.00146
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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MYPN | - | - |
GRCh38 GRCh37 |
1519 | 1568 |
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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Conflicting interpretations of pathogenicity (7) |
criteria provided, conflicting classifications
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Dec 1, 2023 | RCV000024504.26 | |
Pathogenic (1) |
no assertion criteria provided
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May 1, 2012 | RCV000043545.5 | |
Likely benign (4) |
criteria provided, single submitter
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Jan 29, 2024 | RCV000043546.17 | |
Conflicting interpretations of pathogenicity (3) |
criteria provided, conflicting classifications
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Feb 26, 2021 | RCV000157381.6 | |
Conflicting interpretations of pathogenicity (3) |
criteria provided, conflicting classifications
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Apr 13, 2019 | RCV000183576.25 | |
Likely benign (1) |
criteria provided, single submitter
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May 7, 2018 | RCV000254553.5 | |
Uncertain significance (1) |
criteria provided, single submitter
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Mar 30, 2021 | RCV003224105.2 |
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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Likely benign
(Jun 24, 2013)
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criteria provided, single submitter
Method: research
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Not provided
Affected status: unknown
Allele origin:
unknown
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Biesecker Lab/Clinical Genomics Section, National Institutes of Health
Study: ClinSeq
Accession: SCV000051410.1 First in ClinVar: Jun 08, 2015 Last updated: Jun 08, 2015 |
Number of individuals with the variant: 2
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Uncertain significance
(Apr 21, 2017)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: yes
Allele origin:
germline
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Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute
Accession: SCV000740630.1
First in ClinVar: Apr 14, 2018 Last updated: Apr 14, 2018 |
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Uncertain significance
(Nov 19, 2015)
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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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Eurofins Ntd Llc (ga)
Accession: SCV000331381.4
First in ClinVar: Dec 06, 2016 Last updated: Dec 15, 2018 |
Number of individuals with the variant: 1
Sex: mixed
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Uncertain significance
(Apr 13, 2019)
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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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ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV000885813.2
First in ClinVar: Dec 15, 2018 Last updated: Feb 09, 2020 |
Comment:
The p.Tyr20Cys variant (rs140148105) was reported in two patients with either HCM or DCM (Purevjav 2012) and one with DCM who had undergone heart transplant … (more)
The p.Tyr20Cys variant (rs140148105) was reported in two patients with either HCM or DCM (Purevjav 2012) and one with DCM who had undergone heart transplant surgery (Cuenca 2016). This variant is listed in the Genome Aggregation Database (gnomAD) with a frequency of 0.15 percent in the European Non-Finnish population (identified on 200 out of 129,122 chromosomes) and has been reported to the ClinVar database (Variation ID: 31811). This variant was reported to change expression of human MYPN binding proteins and resulted in hypertrophy of the mouse heart (Purevjav 2012). The tyrosine at position 20 is highly conserved and computational analyses of the effects of the p.Tyr20Cys variant on protein structure and function provide conflicting results (SIFT: tolerated, PolyPhen-2: probably damaging). Altogether, there is not enough evidence to classify the p.Tyr20Cys variant with certainty. References: Cuenca S et al. Genetic basis of familial dilated cardiomyopathy patients undergoing heart transplantation. J Heart Lung Transplant. 2016 May;35(5):625-35. Purevjav E et al. Molecular basis for clinical heterogeneity in inherited cardiomyopathies due to myopalladin mutations. Hum Mol Genet. 2012 May 1;21(9):2039-53. (less)
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Uncertain significance
(Feb 26, 2021)
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criteria provided, single submitter
Method: clinical testing
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Primary dilated cardiomyopathy
Affected status: yes
Allele origin:
somatic
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Loeys Lab, Universiteit Antwerpen
Accession: SCV001572575.1
First in ClinVar: Apr 30, 2021 Last updated: Apr 30, 2021 |
Comment:
This sequence change results in a missense variant in the MYPN gene (p.(Tyr20Cys)). This variant is present in population databases with a prevalence of 264/282778 … (more)
This sequence change results in a missense variant in the MYPN gene (p.(Tyr20Cys)). This variant is present in population databases with a prevalence of 264/282778 in GnomAD (BS1). The variant affects a highly conserved nucleotide and highly conserved amino acid. This variant has been reported in the literature. It has been identified in several unrelated individuals with DCM or HCM (PMID: 22286171). In a mouse model the variant resulted in the development of HCM, disruption of intercalated discs and disturbed expression of desmin, desmoplakin, connexin 43 and vinculin, leading to abnormal assembly of the terminal Z-disc(PMID: 22286171) (PS3). Prediction programs predict a pathogenic effect (Align GVGD C65, pathogenic; Polyphen-2-HumDiv: probably damaging; Polyphen-2-HumVar: probably damaging; SIFT: deleterious; Mutation Taster: disease causing) (PP3). The variant was identified in 3 unrelated patients. The first had DCM and an additional TMEM c.1073C>T variant (classified as pathogenic, BP5), a second patient presented with DCM and a third patient presented with HCM and carried an additional MYBPC3 variant (c.1227-2A>G, classified as likely pathogenic). No data on segregation are available. In conclusion this variant was classified as a variant of unknown significance according to ACMG-guidelines (the criteria for benign and pathogenic are contradictory: BS1; BP5; PS3; PP3). (less)
Number of individuals with the variant: 4
Indication for testing: Primary dilated cardiomyopathy
Family history: yes
Sex: male
Tissue: blood
Secondary finding: no
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Likely benign
(Nov 16, 2020)
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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: SCV000236045.11
First in ClinVar: Jul 05, 2015 Last updated: Dec 19, 2017 |
Comment:
This variant is associated with the following publications: (PMID: 23299917, 23861362, 22286171, 26688388, 27171814, 28082330, 26899768, 26498160, 27896284, 22892539, 29875424, 30847666, 32880476)
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Uncertain significance
(Mar 30, 2021)
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criteria provided, single submitter
Method: clinical testing
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Dilated cardiomyopathy 1KK
Dilated cardiomyopathy 1KK Dilated cardiomyopathy 1KK MYPN-related myopathy
Affected status: unknown
Allele origin:
germline
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Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago
Accession: SCV003920263.1
First in ClinVar: Apr 30, 2023 Last updated: Apr 30, 2023 |
Comment:
MYPN NM_032578.3 exon 2 p.Tyr20Cys (c.59A>G): This variant has been reported in the literature in two individuals with DCM and in one individual with HCM … (more)
MYPN NM_032578.3 exon 2 p.Tyr20Cys (c.59A>G): This variant has been reported in the literature in two individuals with DCM and in one individual with HCM (Purevjav 2012 PMID 22286171; Cuenca 2016 PMID 26899768). However, this variant is also present in 0.1% (200/129122) of European alleles in the Genome Aggregation Database (http://gnomad.broadinstitute.org/variant/10-69881254-A-G) and is present in ClinVar, with classifications ranging from likely benign to likely pathogenic (Variation ID:31811). Evolutionary conservation and computational predictive tools suggest that this variant may impact the protein. In addition, an in vivo functional study using transgenic mice supports a deleterious effect of this variant (Purevjav 2012 PMID 22286171). In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain. (less)
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Likely benign
(Dec 01, 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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Revvity Omics, Revvity
Accession: SCV003810983.2
First in ClinVar: Mar 04, 2023 Last updated: Feb 04, 2024 |
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Likely benign
(Jan 29, 2024)
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criteria provided, single submitter
Method: clinical testing
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Dilated cardiomyopathy 1KK
Affected status: unknown
Allele origin:
germline
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Invitae
Accession: SCV000563297.9
First in ClinVar: Nov 10, 2016 Last updated: Feb 20, 2024 |
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Uncertain significance
(Jul 01, 2023)
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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: SCV004033046.5
First in ClinVar: Sep 16, 2023 Last updated: Apr 15, 2024 |
Comment:
MYPN: PP3
Number of individuals with the variant: 1
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Likely benign
(Dec 18, 2018)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: not provided
Allele origin:
germline
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Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Accession: SCV000272189.3
First in ClinVar: May 29, 2016 Last updated: Aug 26, 2019 |
Comment:
The p.Tyr20Cys variant in MYPN is classified as likely benign because it has bee n identified in 0.15% (200/129122) of European chromosomes by gnomAD (http://gno … (more)
The p.Tyr20Cys variant in MYPN is classified as likely benign because it has bee n identified in 0.15% (200/129122) of European chromosomes by gnomAD (http://gno mad.broadinstitute.org). ACMG/AMP criteria applied: PP3, PS3_P, BS1 (less)
Number of individuals with the variant: 2
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Likely benign
(Aug 29, 2017)
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criteria provided, single submitter
Method: clinical testing
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Dilated cardiomyopathy
Affected status: yes
Allele origin:
germline
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Center for Advanced Laboratory Medicine, UC San Diego Health, University of California San Diego
Accession: SCV000995308.1
First in ClinVar: Oct 12, 2019 Last updated: Oct 12, 2019 |
Number of individuals with the variant: 1
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Likely benign
(May 07, 2018)
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criteria provided, single submitter
Method: clinical testing
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Cardiovascular phenotype
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV000317483.6
First in ClinVar: Oct 02, 2016 Last updated: Nov 29, 2022 |
Comment:
This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, … (more)
This alteration is classified as likely 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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Uncertain significance
(Apr 12, 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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Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV001716064.3
First in ClinVar: Jun 15, 2021 Last updated: Jan 26, 2024 |
Comment:
BS1, PS3_moderate
Number of individuals with the variant: 7
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Pathogenic
(May 01, 2012)
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no assertion criteria provided
Method: literature only
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CARDIOMYOPATHY, FAMILIAL HYPERTROPHIC, 22
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000071258.2
First in ClinVar: May 26, 2013 Last updated: Nov 06, 2016 |
Comment on evidence:
In a 59-year-old man with hypertrophic cardiomyopathy (CMH22; see 615248) and in a 58-year-old man with dilated cardiomyopathy (CMD1KK; 615248), both of whom were sporadic … (more)
In a 59-year-old man with hypertrophic cardiomyopathy (CMH22; see 615248) and in a 58-year-old man with dilated cardiomyopathy (CMD1KK; 615248), both of whom were sporadic patients diagnosed at age 45 years and 52 years, respectively, Purevjav et al. (2012) identified heterozygosity for a 59A-G transition in exon 2 of the MYPN gene, resulting in a tyr20-to-cys (Y20C) substitution at an evolutionarily conserved residue in the CARP (ANKRD1; 609599)-binding domain. Transgenic mice with cardiac-restricted overexpression of the Y20C mutation developed CMH and exhibited disrupted intercalated discs as well as disturbed expression of desmin (DES; 125660), desmoplakin (DSP; 125647), connexin-43 (GJA1; 121014), and vinculin (VCL; 193065). Mutant Y20C MYPN also failed to translocate to the nucleus and showed reduced CARP binding compared to wildtype in both in vitro and in vivo systems. Purevjav et al. (2012) noted that during the course of their study, the Y20C variant was described as a SNP (rs14018105) in the 1000 Genomes Pilot Database, with a low A/G genotype frequency (0.001). (less)
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Pathogenic
(May 01, 2012)
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no assertion criteria provided
Method: literature only
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CARDIOMYOPATHY, DILATED, 1KK
Affected status: not provided
Allele origin:
germline
|
OMIM
Accession: SCV000071259.2
First in ClinVar: May 26, 2013 Last updated: Nov 06, 2016 |
Comment on evidence:
In a 59-year-old man with hypertrophic cardiomyopathy (CMH22; see 615248) and in a 58-year-old man with dilated cardiomyopathy (CMD1KK; 615248), both of whom were sporadic … (more)
In a 59-year-old man with hypertrophic cardiomyopathy (CMH22; see 615248) and in a 58-year-old man with dilated cardiomyopathy (CMD1KK; 615248), both of whom were sporadic patients diagnosed at age 45 years and 52 years, respectively, Purevjav et al. (2012) identified heterozygosity for a 59A-G transition in exon 2 of the MYPN gene, resulting in a tyr20-to-cys (Y20C) substitution at an evolutionarily conserved residue in the CARP (ANKRD1; 609599)-binding domain. Transgenic mice with cardiac-restricted overexpression of the Y20C mutation developed CMH and exhibited disrupted intercalated discs as well as disturbed expression of desmin (DES; 125660), desmoplakin (DSP; 125647), connexin-43 (GJA1; 121014), and vinculin (VCL; 193065). Mutant Y20C MYPN also failed to translocate to the nucleus and showed reduced CARP binding compared to wildtype in both in vitro and in vivo systems. Purevjav et al. (2012) noted that during the course of their study, the Y20C variant was described as a SNP (rs14018105) in the 1000 Genomes Pilot Database, with a low A/G genotype frequency (0.001). (less)
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Likely benign
(Oct 09, 2014)
|
no assertion criteria provided
Method: clinical testing
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Primary dilated cardiomyopathy
Affected status: yes
Allele origin:
germline
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Blueprint Genetics
Accession: SCV000207119.1
First in ClinVar: Feb 07, 2015 Last updated: Feb 07, 2015 |
Number of individuals with the variant: 1
|
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Likely pathogenic
(Jun 27, 2013)
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no assertion criteria provided
Method: literature only
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Dilated cardiomyopathy 1KK
Affected status: yes
Allele origin:
germline
|
ClinVar Staff, National Center for Biotechnology Information (NCBI)
Accession: SCV000243996.1
First in ClinVar: Feb 02, 2016 Last updated: Feb 02, 2016 |
|
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Uncertain significance
(Apr 29, 2016)
|
no assertion criteria provided
Method: research
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Dilated cardiomyopathy 1KK
Affected status: yes
Allele origin:
maternal
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Division of Human Genetics, Children's Hospital of Philadelphia
Study: CSER-PediSeq
Accession: SCV000536916.1 First in ClinVar: Apr 22, 2017 Last updated: Apr 22, 2017 |
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not provided
(Apr 27, 2012)
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no classification provided
Method: curation
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not specified
Affected status: not provided
Allele origin:
germline,
de novo
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Leiden Muscular Dystrophy (MYPN)
Accession: SCV000045808.1
First in ClinVar: Apr 04, 2013 Last updated: Apr 04, 2013 |
Observation 1: Observation 2: |
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Germline Functional Evidence
Functional
Help
The functional consequence of the variant, based on experimental evidence and provided by the submitter. consequence |
Method
Help
A brief description of the method used to determine the functional consequence of the variant. A citation for the method is included, when provided by the submitter. |
Result
Help
A brief description of the result of this method for 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 functional evidence for the germline classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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has functional consequence
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Leiden Muscular Dystrophy (MYPN)
Accession: SCV000045808.1
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Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Structural and signaling proteins in the Z-disk and their role in cardiomyopathies. | Noureddine M | Frontiers in physiology | 2023 | PMID: 36935760 |
Genetic Evaluation of A Nation-Wide Dutch Pediatric DCM Cohort: The Use of Genetic Testing in Risk Stratification. | van der Meulen MH | Circulation. Genomic and precision medicine | 2022 | PMID: 36178741 |
Diagnostic yield of genetic testing in heart transplant recipients with prior cardiomyopathy. | Boen HM | The Journal of heart and lung transplantation : the official publication of the International Society for Heart Transplantation | 2022 | PMID: 35581137 |
Understanding the molecular basis of cardiomyopathy. | Bang ML | American journal of physiology. Heart and circulatory physiology | 2022 | PMID: 34797172 |
Implications of Genetic Testing in Dilated Cardiomyopathy. | Verdonschot JAJ | Circulation. Genomic and precision medicine | 2020 | PMID: 32880476 |
Analyses of more than 60,000 exomes questions the role of numerous genes previously associated with dilated cardiomyopathy. | Nouhravesh N | Molecular genetics & genomic medicine | 2016 | PMID: 27896284 |
Genetic basis of familial dilated cardiomyopathy patients undergoing heart transplantation. | Cuenca S | The Journal of heart and lung transplantation : the official publication of the International Society for Heart Transplantation | 2016 | PMID: 26899768 |
Diagnostic yield of molecular autopsy in patients with sudden arrhythmic death syndrome using targeted exome sequencing. | Nunn LM | Europace : European pacing, arrhythmias, and cardiac electrophysiology : journal of the working groups on cardiac pacing, arrhythmias, and cardiac cellular electrophysiology of the European Society of Cardiology | 2016 | PMID: 26498160 |
Interpreting secondary cardiac disease variants in an exome cohort. | Ng D | Circulation. Cardiovascular genetics | 2013 | PMID: 23861362 |
New population-based exome data are questioning the pathogenicity of previously cardiomyopathy-associated genetic variants. | Andreasen C | European journal of human genetics : EJHG | 2013 | PMID: 23299917 |
Molecular basis for clinical heterogeneity in inherited cardiomyopathies due to myopalladin mutations. | Purevjav E | Human molecular genetics | 2012 | PMID: 22286171 |
http://web.expasy.org/variant_pages/VAR_069642.html | - | - | - | - |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=MYPN | - | - | - | - |
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Text-mined citations for rs140148105 ...
HelpRecord last updated Apr 15, 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.