In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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) performed at Invitae indicates that this missense variant is expected to disrupt ZMYND11 protein function. This variant has not been reported in the literature in individuals affected with ZMYND11-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 120 of the ZMYND11 protein (p.Arg120Cys).
ClinVar Genomic variation as it relates to human health
NM_001370100.5(ZMYND11):c.358C>T (p.Arg120Cys)
Germline
Classification
Help
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.
(1)
Help
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
1
criteria provided, single submitter
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_001370100.5(ZMYND11):c.358C>T (p.Arg120Cys)
Variation ID: 2720047 Accession: VCV002720047.1
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 10p15.3 10: 221276 (GRCh38) [ NCBI UCSC ] 10: 267216 (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 Feb 14, 2024 Feb 14, 2024 Jun 27, 2023 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_001370100.5:c.358C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001357029.1:p.Arg120Cys missense NM_001161482.1:c.358C>T NP_001154954.1:p.Arg120Cys missense NM_001202464.3:c.276+11228C>T intron variant NM_001202465.3:c.276+11228C>T intron variant NM_001202466.3:c.276+11228C>T intron variant NM_001202467.1:c.276+11228C>T intron variant NM_001202468.1:c.358C>T NP_001189397.1:p.Arg120Cys missense NM_001330057.3:c.307C>T NP_001316986.1:p.Arg103Cys missense NM_001370097.3:c.358C>T NP_001357026.1:p.Arg120Cys missense NM_001370098.2:c.358C>T NP_001357027.1:p.Arg120Cys missense NM_001370099.2:c.358C>T NP_001357028.1:p.Arg120Cys missense NM_001370101.2:c.358C>T NP_001357030.1:p.Arg120Cys missense NM_001370102.2:c.358C>T NP_001357031.1:p.Arg120Cys missense NM_001370103.2:c.276+11228C>T intron variant NM_001370104.2:c.276+11228C>T intron variant NM_001370105.2:c.276+11228C>T intron variant NM_001370106.2:c.276+11228C>T intron variant NM_001370107.2:c.276+11228C>T intron variant NM_001370108.2:c.276+11228C>T intron variant NM_001370109.2:c.276+11228C>T intron variant NM_001370110.2:c.276+11228C>T intron variant NM_001370111.2:c.276+11228C>T intron variant NM_001370112.2:c.307C>T NP_001357041.1:p.Arg103Cys missense NM_001370113.2:c.358C>T NP_001357042.1:p.Arg120Cys missense NM_001370114.2:c.358C>T NP_001357043.1:p.Arg120Cys missense NM_001370115.2:c.358C>T NP_001357044.1:p.Arg120Cys missense NM_001370116.2:c.292C>T NP_001357045.1:p.Arg98Cys missense NM_001370117.2:c.358C>T NP_001357046.1:p.Arg120Cys missense NM_001370118.2:c.238C>T NP_001357047.1:p.Arg80Cys missense NM_001370119.2:c.358C>T NP_001357048.1:p.Arg120Cys missense NM_001370120.2:c.210+11228C>T intron variant NM_001370121.2:c.156+11228C>T intron variant NM_001370122.2:c.276+11228C>T intron variant NM_001370123.2:c.225+11228C>T intron variant NM_001370124.3:c.-33-15562C>T intron variant NM_006624.7:c.358C>T NP_006615.2:p.Arg120Cys missense NM_212479.4:c.358C>T NP_997644.2:p.Arg120Cys missense NR_163254.2:n.445C>T non-coding transcript variant NC_000010.11:g.221276C>T NC_000010.10:g.267216C>T NG_029960.1:g.91812C>T - Protein change
- R103C, R120C, R80C, R98C
- Other names
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- Canonical SPDI
- NC_000010.11:221275: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
Help
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 | ||
|---|---|---|---|---|---|---|
| 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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| ZMYND11 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
226 | 362 | |
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. |
|---|---|---|---|---|
| Uncertain significance (1) |
criteria provided, single submitter
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Jun 27, 2023 | RCV003546315.2 |
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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|---|---|---|---|---|---|
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Uncertain significance
(Jun 27, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV004275154.1
First in ClinVar: Feb 14, 2024 Last updated: Feb 14, 2024 |
Comment:
In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant … (more)
In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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) performed at Invitae indicates that this missense variant is expected to disrupt ZMYND11 protein function. This variant has not been reported in the literature in individuals affected with ZMYND11-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 120 of the ZMYND11 protein (p.Arg120Cys). (less)
|
Comment:
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. |
Comment:
In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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) performed at Invitae indicates that this missense variant is expected to disrupt ZMYND11 protein function. This variant has not been reported in the literature in individuals affected with ZMYND11-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 120 of the ZMYND11 protein (p.Arg120Cys).
Citations for germline classification of this variant
Help| There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar. |
Text-mined citations for this variant ...
HelpRecord last updated Sep 30, 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.