ClinVar Genomic variation as it relates to human health
NM_001370100.5(ZMYND11):c.876_882del (p.Phe293fs)
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.876_882del (p.Phe293fs)
Variation ID: 2503414 Accession: VCV002503414.4
- Type and length
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Microsatellite, 7 bp
- Location
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Cytogenetic: 10p15.3 10: 242057-242063 (GRCh38) [ NCBI UCSC ] 10: 287997-288003 (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 Aug 26, 2023 Sep 16, 2023 Aug 18, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001370100.5:c.876_882del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001357029.1:p.Phe293fs frameshift NM_001161482.1:c.869_875GTTTTGG[1] NP_001154954.1:p.Phe293Glnfs frameshift NM_001202464.3:c.714_720del NP_001189393.1:p.Phe239fs frameshift NM_001202465.3:c.621_627del NP_001189394.1:p.Phe208fs frameshift NM_001202466.3:c.711_717del NP_001189395.1:p.Phe238fs frameshift NM_001202467.1:c.714_720del NP_001189396.1:p.Phe239fs frameshift NM_001202468.1:c.876_882del NP_001189397.1:p.Phe293fs frameshift NM_001330057.3:c.825_831del NP_001316986.1:p.Phe276fs frameshift NM_001370097.3:c.876_882del NP_001357026.1:p.Phe293fs frameshift NM_001370098.2:c.876_882del NP_001357027.1:p.Phe293fs frameshift NM_001370099.2:c.876_882del NP_001357028.1:p.Phe293fs frameshift NM_001370101.2:c.876_882del NP_001357030.1:p.Phe293fs frameshift NM_001370102.2:c.876_882del NP_001357031.1:p.Phe293fs frameshift NM_001370103.2:c.714_720del NP_001357032.1:p.Phe239fs frameshift NM_001370104.2:c.714_720del NP_001357033.1:p.Phe239fs frameshift NM_001370105.2:c.714_720del NP_001357034.1:p.Phe239fs frameshift NM_001370106.2:c.714_720del NP_001357035.1:p.Phe239fs frameshift NM_001370107.2:c.714_720del NP_001357036.1:p.Phe239fs frameshift NM_001370108.2:c.714_720del NP_001357037.1:p.Phe239fs frameshift NM_001370109.2:c.714_720del NP_001357038.1:p.Phe239fs frameshift NM_001370110.2:c.621_627del NP_001357039.1:p.Phe208fs frameshift NM_001370111.2:c.711_717del NP_001357040.1:p.Phe238fs frameshift NM_001370112.2:c.825_831del NP_001357041.1:p.Phe276fs frameshift NM_001370113.2:c.783_789del NP_001357042.1:p.Phe262fs frameshift NM_001370114.2:c.783_789del NP_001357043.1:p.Phe262fs frameshift NM_001370115.2:c.873_879del NP_001357044.1:p.Phe292fs frameshift NM_001370116.2:c.810_816del NP_001357045.1:p.Phe271fs frameshift NM_001370117.2:c.876_882del NP_001357046.1:p.Phe293fs frameshift NM_001370118.2:c.756_762del NP_001357047.1:p.Phe253fs frameshift NM_001370119.2:c.798_804del NP_001357048.1:p.Phe267fs frameshift NM_001370120.2:c.648_654del NP_001357049.1:p.Phe217fs frameshift NM_001370121.2:c.594_600del NP_001357050.1:p.Phe199fs frameshift NM_001370122.2:c.570_576del NP_001357051.1:p.Phe191fs frameshift NM_001370123.2:c.519_525del NP_001357052.1:p.Phe174fs frameshift NM_001370124.3:c.405_411del NP_001357053.1:p.Phe136fs frameshift NM_006624.7:c.876_882del NP_006615.2:p.Phe293fs frameshift NM_212479.4:c.873_879del NP_997644.2:p.Phe292fs frameshift NR_163254.2:n.900GTTTTGG[1] non-coding transcript variant NC_000010.11:g.242058GTTTTGG[1] NC_000010.10:g.287998GTTTTGG[1] NG_029960.1:g.112594GTTTTGG[1] - Protein change
- F136fs, F174fs, F191fs, F199fs, F208fs, F217fs, F238fs, F239fs, F253fs, F262fs, F267fs, F271fs, F276fs, F292fs, F293fs
- Other names
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- Canonical SPDI
- NC_000010.11:242056:GGTTTTGGGTTTTGG:GGTTTTGG
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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
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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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 |
Conditions - Germline
Condition
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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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Pathogenic (1) |
criteria provided, single submitter
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Aug 18, 2023 | RCV003322937.3 | |
Pathogenic (1) |
no assertion criteria provided
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Apr 1, 2023 | RCV003326687.1 |
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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Pathogenic
(Aug 18, 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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GeneDx
Accession: SCV004028084.1
First in ClinVar: Aug 26, 2023 Last updated: Aug 26, 2023 |
Comment:
Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of … (more)
Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); Has not been previously published as pathogenic or benign to our knowledge (less)
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Pathogenic
(Apr 01, 2023)
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no assertion criteria provided
Method: clinical testing
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Intellectual disability, autosomal dominant 30
Affected status: yes
Allele origin:
germline
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Clinical Laboratory Sciences Program (CLSP), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS)
Accession: SCV003927820.1
First in ClinVar: Sep 16, 2023 Last updated: Sep 16, 2023 |
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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 Sep 16, 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.