ClinVar Genomic variation as it relates to human health
NM_001384528.1(GATAD2A):c.1873C>T (p.Arg625Cys)
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_001384528.1(GATAD2A):c.1873C>T (p.Arg625Cys)
Variation ID: 2411844 Accession: VCV002411844.2
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 19p13.11 19: 19505442 (GRCh38) [ NCBI UCSC ] 19: 19616251 (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 8, 2023 May 1, 2024 Oct 3, 2022 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001384528.1:c.1873C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001371457.1:p.Arg625Cys missense NM_001300946.3:c.1873C>T NP_001287875.1:p.Arg625Cys missense NM_001359631.2:c.1798C>T NP_001346560.1:p.Arg600Cys missense NM_001384511.1:c.1873C>T NP_001371440.1:p.Arg625Cys missense NM_001384512.1:c.1873C>T NP_001371441.1:p.Arg625Cys missense NM_001384513.1:c.1873C>T NP_001371442.1:p.Arg625Cys missense NM_001384514.1:c.1873C>T NP_001371443.1:p.Arg625Cys missense NM_001384515.1:c.1873C>T NP_001371444.1:p.Arg625Cys missense NM_001384516.1:c.1873C>T NP_001371445.1:p.Arg625Cys missense NM_001384517.1:c.1873C>T NP_001371446.1:p.Arg625Cys missense NM_001384518.1:c.1873C>T NP_001371447.1:p.Arg625Cys missense NM_001384519.1:c.1873C>T NP_001371448.1:p.Arg625Cys missense NM_001384521.1:c.1873C>T NP_001371450.1:p.Arg625Cys missense NM_001384522.1:c.1873C>T NP_001371451.1:p.Arg625Cys missense NM_001384523.1:c.1873C>T NP_001371452.1:p.Arg625Cys missense NM_001384524.1:c.1873C>T NP_001371453.1:p.Arg625Cys missense NM_001384525.1:c.1873C>T NP_001371454.1:p.Arg625Cys missense NM_001384526.1:c.1873C>T NP_001371455.1:p.Arg625Cys missense NM_001384527.1:c.1873C>T NP_001371456.1:p.Arg625Cys missense NM_001384529.1:c.1870C>T NP_001371458.1:p.Arg624Cys missense NM_001384530.1:c.1870C>T NP_001371459.1:p.Arg624Cys missense NM_001384531.1:c.1870C>T NP_001371460.1:p.Arg624Cys missense NM_001384532.1:c.1870C>T NP_001371461.1:p.Arg624Cys missense NM_001384533.1:c.1870C>T NP_001371462.1:p.Arg624Cys missense NM_001384534.1:c.1798C>T NP_001371463.1:p.Arg600Cys missense NM_001384535.1:c.1798C>T NP_001371464.1:p.Arg600Cys missense NM_001384536.1:c.1798C>T NP_001371465.1:p.Arg600Cys missense NM_001384537.1:c.2026C>T NP_001371466.1:p.Arg676Cys missense NM_001384538.1:c.1795C>T NP_001371467.1:p.Arg599Cys missense NM_001384539.1:c.1783C>T NP_001371468.1:p.Arg595Cys missense NM_001384540.1:c.1444C>T NP_001371469.1:p.Arg482Cys missense NM_001384541.1:c.1444C>T NP_001371470.1:p.Arg482Cys missense NM_017660.5:c.1870C>T NP_060130.3:p.Arg624Cys missense NR_169268.1:n.2337C>T non-coding transcript variant NC_000019.10:g.19505442C>T NC_000019.9:g.19616251C>T NG_140851.1:g.550C>T - Protein change
- R595C, R599C, R600C, R625C, R482C, R676C, R624C
- Other names
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- Canonical SPDI
- NC_000019.10:19505441: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
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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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GATAD2A | - | - |
GRCh38 GRCh37 |
51 | 73 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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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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Oct 3, 2022 | RCV004247040.1 |
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
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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
(Oct 03, 2022)
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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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Ambry Genetics
Accession: SCV003756613.2
First in ClinVar: Feb 07, 2023 Last updated: May 01, 2024 |
Comment:
The c.1870C>T (p.R624C) alteration is located in exon 12 (coding exon 11) of the GATAD2A gene. This alteration results from a C to T substitution … (more)
The c.1870C>T (p.R624C) alteration is located in exon 12 (coding exon 11) of the GATAD2A gene. This alteration results from a C to T substitution at nucleotide position 1870, causing the arginine (R) at amino acid position 624 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. (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 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.