ClinVar Genomic variation as it relates to human health
NM_002473.6(MYH9):c.4270G>A (p.Asp1424Asn)
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_002473.6(MYH9):c.4270G>A (p.Asp1424Asn)
Variation ID: 14082 Accession: VCV000014082.22
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 22q12.3 22: 36292060 (GRCh38) [ NCBI UCSC ] 22: 36688106 (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 Nov 24, 2024 Sep 18, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_002473.6:c.4270G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_002464.1:p.Asp1424Asn missense NC_000022.11:g.36292060C>T NC_000022.10:g.36688106C>T NG_011884.2:g.100959G>A LRG_567:g.100959G>A LRG_567t1:c.4270G>A LRG_567p1:p.Asp1424Asn P35579:p.Asp1424Asn - Protein change
- D1424N
- Other names
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- Canonical SPDI
- NC_000022.11:36292059: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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Allele frequency
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The frequency of the allele represented by this VCV record.
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- 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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MYH9 | Little evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
1392 | 1498 |
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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Pathogenic (6) |
criteria provided, multiple submitters, no conflicts
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Nov 17, 2023 | RCV000015134.43 | |
Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Aug 18, 2023 | RCV000790358.4 | |
Pathogenic (1) |
criteria provided, single submitter
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May 27, 2020 | RCV001271110.2 | |
Likely pathogenic (1) |
criteria provided, single submitter
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May 31, 2021 | RCV002466404.1 | |
Pathogenic (3) |
criteria provided, multiple submitters, no conflicts
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Sep 18, 2024 | RCV002513058.5 | |
Pathogenic (1) |
criteria provided, single submitter
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Dec 21, 2021 | RCV002496364.1 |
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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Pathogenic
(Dec 12, 2018)
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criteria provided, single submitter
Method: research
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MYH9-related disorder
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
unknown
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NIHR Bioresource Rare Diseases, University of Cambridge
Accession: SCV000891151.1
First in ClinVar: Jul 27, 2019 Last updated: Jul 27, 2019 |
Comment:
PS4, PP1_strong, PM2, PP4, PP3
Observation 1:
Sex: male
Ethnicity/Population group: Middle-Eastern
Observation 2:
Sex: male
Observation 3:
Sex: male
Ethnicity/Population group: South-Asian
Observation 4:
Sex: female
Ethnicity/Population group: Hispanic
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Pathogenic
(Dec 21, 2021)
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criteria provided, single submitter
Method: clinical testing
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Macrothrombocytopenia and granulocyte inclusions with or without nephritis or sensorineural hearing loss
Autosomal dominant nonsyndromic hearing loss 17
Affected status: unknown
Allele origin:
unknown
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Fulgent Genetics, Fulgent Genetics
Accession: SCV002803145.1
First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022 |
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Pathogenic
(Aug 18, 2023)
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criteria provided, single submitter
Method: clinical testing
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MYH9-related condition
Affected status: unknown
Allele origin:
germline
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PreventionGenetics, part of Exact Sciences
Accession: SCV004107706.1
First in ClinVar: Nov 20, 2023 Last updated: Nov 20, 2023 |
Comment:
The MYH9 c.4270G>A variant is predicted to result in the amino acid substitution p.Asp1424Asn. This variant has been reported to be causative for MYH9-related disorders … (more)
The MYH9 c.4270G>A variant is predicted to result in the amino acid substitution p.Asp1424Asn. This variant has been reported to be causative for MYH9-related disorders in several unrelated families (see for example Kunishima et al. 2001. PubMed ID: 11159552; Seri et al. 2003. PubMed ID: 12792306; Dong et al. 2005. PubMed ID: 16098078; Verver et al. 2016. PubMed ID: 26226608). The c.4270G>A substitution is one of the most common pathogenic variants found in the MYH9 gene, and it is thought to cause disease due to haploinsufficiency from unstable MYH9 protein (Deutsch et al. 2003. PubMed ID: 12649151). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. This variant is interpreted as pathogenic. (less)
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Pathogenic
(Jul 25, 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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GeneDx
Accession: SCV003923969.2
First in ClinVar: May 13, 2023 Last updated: Sep 29, 2024 |
Comment:
Published functional studies demonstrate a damaging effect on platelet count, platelet size, and bleeding time (PMID: 35584211, 32315395, 21908426); Not observed at significant frequency in … (more)
Published functional studies demonstrate a damaging effect on platelet count, platelet size, and bleeding time (PMID: 35584211, 32315395, 21908426); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 30725031, 31064749, 23207509, 22217922, 22967416, 27577209, 26226608, 26942920, 29451856, 32581362, 33855781, 34711033, 34711031, 35295078, 16162639, 24186861, 12649151, 21908426, 32315395, 15339844, 19572073, 35584211, 11159552) (less)
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Pathogenic
(Dec 29, 2016)
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criteria provided, single submitter
Method: clinical testing
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May-Hegglin anomaly
Affected status: yes
Allele origin:
germline
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Genetic Services Laboratory, University of Chicago
Accession: SCV000595889.1
First in ClinVar: Jun 02, 2016 Last updated: Jun 02, 2016 |
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Pathogenic
(May 27, 2020)
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criteria provided, single submitter
Method: clinical testing
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Thrombocytopenia
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
inherited
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MNM Diagnostics
Accession: SCV001451954.1
First in ClinVar: Jan 02, 2021 Last updated: Jan 02, 2021 |
Comment:
According to ACMG Guidelines, the variant meets the following criteria of pathogenicity: PS4, PM2, PM5, PP2, PP3, PP4, PP5.
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Pathogenic
(-)
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criteria provided, single submitter
Method: clinical testing
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Macrothrombocytopenia and granulocyte inclusions with or without nephritis or sensorineural hearing loss
Affected status: yes
Allele origin:
maternal,
unknown
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ISTH-SSC Genomics in Thrombosis and Hemostasis, KU Leuven, Center for Molecular and Vascular Biology
Accession: SCV002500896.1
First in ClinVar: Apr 23, 2022 Last updated: Apr 23, 2022
Comment:
GoldVariant submitters: Dr Karyn Mégy, NIHR Bioresource - Cambridge University, UK and Marie-Christine Morel-Kopp, Northern Blood Research Centre, Sydney, Australia
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Observation 1:
Family history: yes
Observation 2: Observation 3:
Clinical Features:
Macrothrombocytopenia (present) , Döhle body-like inclusions (present)
Ethnicity/Population group: Caucasian
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Likely pathogenic
(May 31, 2021)
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criteria provided, single submitter
Method: clinical testing
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Autosomal dominant nonsyndromic hearing loss 17
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
germline
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Genetics and Molecular Pathology, SA Pathology
Additional submitter:
Shariant Australia, Australian Genomics
Accession: SCV002761846.1
First in ClinVar: Dec 17, 2022 Last updated: Dec 17, 2022 |
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Pathogenic
(-)
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criteria provided, single submitter
Method: clinical testing
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Macrothrombocytopenia and granulocyte inclusions with or without nephritis or sensorineural hearing loss
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
inherited
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Suma Genomics
Accession: SCV003852611.1
First in ClinVar: Apr 01, 2023 Last updated: Apr 01, 2023 |
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Pathogenic
(Nov 17, 2023)
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criteria provided, single submitter
Method: clinical testing
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Macrothrombocytopenia and granulocyte inclusions with or without nephritis or sensorineural hearing loss
Affected status: unknown
Allele origin:
germline
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Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV004222828.1
First in ClinVar: Jan 06, 2024 Last updated: Jan 06, 2024 |
Comment:
Variant summary: MYH9 c.4270G>A (p.Asp1424Asn) results in a conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging … (more)
Variant summary: MYH9 c.4270G>A (p.Asp1424Asn) results in a conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251372 control chromosomes. c.4270G>A has been reported in the literature in multiple individuals affected with Macrothrombocytopenia And Granulocyte Inclusions With Or Without Nephritis Or Sensorineural Hearing Loss (Deutsch_2003, Verver_2016), and it co-segregated with disease conditions in two large families (Deutsch_2003). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in <50% of normal protein levels in patients' cells (Deutsch_2003). The following publications have been ascertained in the context of this evaluation (PMID: 12649151, 26226608). Seven submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. (less)
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Pathogenic
(Dec 11, 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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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV003444536.2
First in ClinVar: Feb 07, 2023 Last updated: Feb 14, 2024 |
Comment:
This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 1424 of the MYH9 protein … (more)
This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 1424 of the MYH9 protein (p.Asp1424Asn). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with MYH9-related disorders (PMID: 11159552, 23207509). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 14082). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on MYH9 protein function. Experimental studies have shown that this missense change affects MYH9 function (PMID: 15339844). For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Sep 18, 2024)
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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: SCV005413401.1
First in ClinVar: Nov 24, 2024 Last updated: Nov 24, 2024 |
Comment:
PP1_moderate, PP3, PP5, PM2_moderate, PM5, PS3, PS4
Number of individuals with the variant: 4
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Pathogenic
(Jul 15, 2003)
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no assertion criteria provided
Method: literature only
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MACROTHROMBOCYTOPENIA AND GRANULOCYTE INCLUSIONS WITH OR WITHOUT NEPHRITIS OR SENSORINEURAL HEARING LOSS
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000035391.3
First in ClinVar: Apr 04, 2013 Last updated: Jun 30, 2018 |
Comment on evidence:
Deutsch et al. (2003) studied a Swiss family and an American family with the May-Hegglin anomaly/Fechtner syndrome (MATINS; 155100) and found an asp1424-to-asn (D1424N) mutation … (more)
Deutsch et al. (2003) studied a Swiss family and an American family with the May-Hegglin anomaly/Fechtner syndrome (MATINS; 155100) and found an asp1424-to-asn (D1424N) mutation in the MYH9 gene. Affected members in both families presented with severe thrombocytopenia, as well as characteristic giant platelets and Dohle-like inclusion bodies on blood smear examination. In the Swiss family, 2 affected sisters developed bilateral cataracts at a young age, whereas the third sister and her son had high-tone sensorineural deafness. Two individuals with thrombocytopenia showed no extrahematologic symptoms. None showed signs of nephritis. In the American family, 4 individuals suffered from sensorineural deafness, but no cataracts or nephritis were observed. Haplotype analysis indicated that in this family the mutation was a de novo event in 1 individual. The same mutation had previously been described in a pedigree of Japanese origin and in 2 pedigrees of American origin, most likely as a result of independent mutation events (Heath et al., 2001; Kunishima et al., 2001). Deutsch et al. (2003) demonstrated that the phenotypes result from a highly unstable MYH9 protein. No abnormalities in protein localization or mRNA stability were observed. They hypothesized that haploinsufficiency of MYH9 results in a failure to properly reorganize the cytoskeleton in megakaryocytes as required for efficient platelet production. In the proband of the family with macrothrombocytopenia and progressive sensorineural deafness reported by Brodie et al. (1992), Mhatre et al. (2003) identified a heterozygous 4270G-A transition in exon 30 of the MYH9 gene, resulting in the D1424N substitution in the highly conserved coiled-coil region of the protein. Seri et al. (2003) identified a heterozygous D1424N mutation in a patient described as having May-Hegglin anomaly and Sebastian syndrome. The authors suggested that the 2 disorders are not separate entities, but rather represent the same disease with a continuous clinical spectrum. (less)
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not provided
(-)
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no classification provided
Method: literature only
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Macrothrombocytopenia and granulocyte inclusions with or without nephritis or sensorineural hearing loss
Affected status: unknown
Allele origin:
germline
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GeneReviews
Accession: SCV000055828.3
First in ClinVar: Apr 04, 2013 Last updated: Oct 01, 2022 |
Comment:
Associated with thrombocytopenia, but low risk of developing other disease manifestations over time
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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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Diagnostic delay of MYH9-related disorder in Japan. | Sakamoto A | British journal of haematology | 2024 | PMID: 38650331 |
Reduced platelet forces underlie impaired hemostasis in mouse models of MYH9-related disease. | Baumann J | Science advances | 2022 | PMID: 35584211 |
GoldVariants, a resource for sharing rare genetic variants detected in bleeding, thrombotic, and platelet disorders: Communication from the ISTH SSC Subcommittee on Genomics in Thrombosis and Hemostasis. | Megy K | Journal of thrombosis and haemostasis : JTH | 2021 | PMID: 34355501 |
MYH9 disorder: Identification and a novel mutation in patients with macrothrombocytopenia. | Natesirinilkul R | Pediatric blood & cancer | 2021 | PMID: 33855781 |
MYH9-Related Disease. | Adam MP | - | 2021 | PMID: 20301740 |
Megakaryocyte migration defects due to nonmuscle myosin IIA mutations underlie thrombocytopenia in MYH9-related disease. | Pal K | Blood | 2020 | PMID: 32315395 |
A D1424N mutation in the MYH9 gene results in macrothrombocytopenia and granulocytic inclusion bodies in a Chinese inherited macrothrombocytopenia pedigree. | Guo X | Clinical chemistry and laboratory medicine | 2018 | PMID: 29451856 |
Diagnosis and treatment of MYH9-RD in an Australasian cohort with thrombocytopenia. | Rabbolini DJ | Platelets | 2018 | PMID: 29090586 |
Late onset and high-frequency dominant hearing loss in a family with MYH9 disorder. | Wasano K | European archives of oto-rhino-laryngology : official journal of the European Federation of Oto-Rhino-Laryngological Societies (EUFOS) : affiliated with the German Society for Oto-Rhino-Laryngology - Head and Neck Surgery | 2016 | PMID: 26942920 |
Nonmuscle Myosin Heavy Chain IIA Mutation Predicts Severity and Progression of Sensorineural Hearing Loss in Patients With MYH9-Related Disease. | Verver EJ | Ear and hearing | 2016 | PMID: 26226608 |
MYH9-related thrombocytopenia and intracranial bleedings: a complex clinical/surgical management and review of the literature. | Palandri F | British journal of haematology | 2015 | PMID: 25752999 |
MYH9-related disease: a novel prognostic model to predict the clinical evolution of the disease based on genotype-phenotype correlations. | Pecci A | Human mutation | 2014 | PMID: 24186861 |
Clinical, pathological, and genetic analysis of ten patients with MYH9-related disease. | Sun XH | Acta haematologica | 2013 | PMID: 23207509 |
Mouse models of MYH9-related disease: mutations in nonmuscle myosin II-A. | Zhang Y | Blood | 2012 | PMID: 21908426 |
Recent advances in the understanding and management of MYH9-related inherited thrombocytopenias. | Balduini CL | British journal of haematology | 2011 | PMID: 21542825 |
MYH9-related disease: Report on five German families and description of a novel mutation. | Savoia A | Annals of hematology | 2010 | PMID: 20221761 |
Megakaryocytes of patients with MYH9-related thrombocytopenia present an altered proplatelet formation. | Pecci A | Thrombosis and haemostasis | 2009 | PMID: 19572073 |
Rod mutations associated with MYH9-related disorders disrupt nonmuscle myosin-IIA assembly. | Franke JD | Blood | 2005 | PMID: 15339844 |
MYH9-related disease: May-Hegglin anomaly, Sebastian syndrome, Fechtner syndrome, and Epstein syndrome are not distinct entities but represent a variable expression of a single illness. | Seri M | Medicine | 2003 | PMID: 12792306 |
Asp1424Asn MYH9 mutation results in an unstable protein responsible for the phenotypes in May-Hegglin anomaly/Fechtner syndrome. | Deutsch S | Blood | 2003 | PMID: 12649151 |
Macrothrombocytopenia and progressive deafness is due to a mutation in MYH9. | Mhatre AN | Otology & neurotology : official publication of the American Otological Society, American Neurotology Society [and] European Academy of Otology and Neurotology | 2003 | PMID: 12621333 |
Nonmuscle myosin heavy chain IIA mutations define a spectrum of autosomal dominant macrothrombocytopenias: May-Hegglin anomaly and Fechtner, Sebastian, Epstein, and Alport-like syndromes. | Heath KE | American journal of human genetics | 2001 | PMID: 11590545 |
Mutations in the NMMHC-A gene cause autosomal dominant macrothrombocytopenia with leukocyte inclusions (May-Hegglin anomaly/Sebastian syndrome). | Kunishima S | Blood | 2001 | PMID: 11159552 |
Macrothrombocytopenia and progressive deafness: a new genetic syndrome. | Brodie HA | The American journal of otology | 1992 | PMID: 1449176 |
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Text-mined citations for rs80338831 ...
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.