ClinVar Genomic variation as it relates to human health
NM_001370100.5(ZMYND11):c.1678A>C (p.Lys560Gln)
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_001370100.5(ZMYND11):c.1678A>C (p.Lys560Gln)
Variation ID: 2664693 Accession: VCV002664693.1
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 10p15.3 10: 249080 (GRCh38) [ NCBI UCSC ] 10: 295020 (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 Dec 17, 2023 Dec 17, 2023 Mar 15, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001370100.5:c.1678A>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001357029.1:p.Lys560Gln missense NM_001161482.1:c.1678A>C NP_001154954.1:p.Lys560Gln missense NM_001202464.3:c.1516A>C NP_001189393.1:p.Lys506Gln missense NM_001202465.3:c.1423A>C NP_001189394.1:p.Lys475Gln missense NM_001202466.3:c.1513A>C NP_001189395.1:p.Lys505Gln missense NM_001202467.1:c.1516A>C NP_001189396.1:p.Lys506Gln missense NM_001202468.1:c.1678A>C NP_001189397.1:p.Lys560Gln missense NM_001330057.3:c.1627A>C NP_001316986.1:p.Lys543Gln missense NM_001370097.3:c.1678A>C NP_001357026.1:p.Lys560Gln missense NM_001370098.2:c.1678A>C NP_001357027.1:p.Lys560Gln missense NM_001370099.2:c.1678A>C NP_001357028.1:p.Lys560Gln missense NM_001370101.2:c.1678A>C NP_001357030.1:p.Lys560Gln missense NM_001370102.2:c.1678A>C NP_001357031.1:p.Lys560Gln missense NM_001370103.2:c.1516A>C NP_001357032.1:p.Lys506Gln missense NM_001370104.2:c.1516A>C NP_001357033.1:p.Lys506Gln missense NM_001370105.2:c.1516A>C NP_001357034.1:p.Lys506Gln missense NM_001370106.2:c.1516A>C NP_001357035.1:p.Lys506Gln missense NM_001370107.2:c.1516A>C NP_001357036.1:p.Lys506Gln missense NM_001370108.2:c.1516A>C NP_001357037.1:p.Lys506Gln missense NM_001370109.2:c.1516A>C NP_001357038.1:p.Lys506Gln missense NM_001370110.2:c.1423A>C NP_001357039.1:p.Lys475Gln missense NM_001370111.2:c.1513A>C NP_001357040.1:p.Lys505Gln missense NM_001370112.2:c.1627A>C NP_001357041.1:p.Lys543Gln missense NM_001370113.2:c.1585A>C NP_001357042.1:p.Lys529Gln missense NM_001370114.2:c.1585A>C NP_001357043.1:p.Lys529Gln missense NM_001370115.2:c.1675A>C NP_001357044.1:p.Lys559Gln missense NM_001370116.2:c.1612A>C NP_001357045.1:p.Lys538Gln missense NM_001370117.2:c.1609A>C NP_001357046.1:p.Lys537Gln missense NM_001370118.2:c.1558A>C NP_001357047.1:p.Lys520Gln missense NM_001370119.2:c.1531A>C NP_001357048.1:p.Lys511Gln missense NM_001370120.2:c.1450A>C NP_001357049.1:p.Lys484Gln missense NM_001370121.2:c.1396A>C NP_001357050.1:p.Lys466Gln missense NM_001370122.2:c.1372A>C NP_001357051.1:p.Lys458Gln missense NM_001370123.2:c.1321A>C NP_001357052.1:p.Lys441Gln missense NM_001370124.3:c.1207A>C NP_001357053.1:p.Lys403Gln missense NM_006624.7:c.1678A>C NP_006615.2:p.Lys560Gln missense NM_212479.4:c.1675A>C NP_997644.2:p.Lys559Gln missense NR_163254.2:n.1709A>C non-coding transcript variant NC_000010.11:g.249080A>C NC_000010.10:g.295020A>C NG_029960.1:g.119616A>C NG_085301.1:g.853A>C - Protein change
- K403Q, K441Q, K458Q, K466Q, K475Q, K484Q, K505Q, K506Q, K511Q, K520Q, K529Q, K537Q, K538Q, K543Q, K559Q, K560Q
- Other names
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- Canonical SPDI
- NC_000010.11:249079:A: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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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
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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
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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 |
208 | 339 | |
LOC126860802 | - | - | - | GRCh38 | - | 97 |
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
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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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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Uncertain significance (1) |
criteria provided, single submitter
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Mar 15, 2023 | RCV003447668.1 |
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
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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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Uncertain significance
(Mar 15, 2023)
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criteria provided, single submitter
Method: clinical testing
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Intellectual disability, autosomal dominant 30
Affected status: yes
Allele origin:
germline
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Genetics and Molecular Pathology, SA Pathology
Additional submitter:
Shariant Australia, Australian Genomics
Accession: SCV004175217.1
First in ClinVar: Dec 17, 2023 Last updated: Dec 17, 2023 |
Comment:
The ZMYND11 c.1678A>C variant is classified as VUS (PS2_Supporting, PM2) The ZMYND11 c.1678A>C variant is a single nucleotide change in exon 14/15 of the ZMYND11 … (more)
The ZMYND11 c.1678A>C variant is classified as VUS (PS2_Supporting, PM2) The ZMYND11 c.1678A>C variant is a single nucleotide change in exon 14/15 of the ZMYND11 gene, which is predicted to change the amino acid lysine at position 560 in the protein to glutamine. This variant has been identified as a de novo variant in this patient, phenotype consistent with gene but not highly specific and high genetic heterogeneity. (PS2_supporting). This variant is absent from population databases (PM2). The variant has been reported in dbSNP (rs758034609). It has not been reported in Clin Var or HGMD. (less)
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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
HelpThere 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 Dec 17, 2023
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.