ClinVar Genomic variation as it relates to human health
NM_001384528.1(GATAD2A):c.1073A>C (p.Lys358Thr)
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.1073A>C (p.Lys358Thr)
Variation ID: 3068649 Accession: VCV003068649.1
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 19p13.11 19: 19498591 (GRCh38) [ NCBI UCSC ] 19: 19609400 (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 15, 2024 Apr 15, 2024 Jun 6, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001384528.1:c.1073A>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001371457.1:p.Lys358Thr missense NM_001300946.3:c.1073A>C NP_001287875.1:p.Lys358Thr missense NM_001359631.2:c.1073A>C NP_001346560.1:p.Lys358Thr missense NM_001384511.1:c.1073A>C NP_001371440.1:p.Lys358Thr missense NM_001384512.1:c.1073A>C NP_001371441.1:p.Lys358Thr missense NM_001384513.1:c.1073A>C NP_001371442.1:p.Lys358Thr missense NM_001384514.1:c.1073A>C NP_001371443.1:p.Lys358Thr missense NM_001384515.1:c.1073A>C NP_001371444.1:p.Lys358Thr missense NM_001384516.1:c.1073A>C NP_001371445.1:p.Lys358Thr missense NM_001384517.1:c.1073A>C NP_001371446.1:p.Lys358Thr missense NM_001384518.1:c.1073A>C NP_001371447.1:p.Lys358Thr missense NM_001384519.1:c.1073A>C NP_001371448.1:p.Lys358Thr missense NM_001384521.1:c.1073A>C NP_001371450.1:p.Lys358Thr missense NM_001384522.1:c.1073A>C NP_001371451.1:p.Lys358Thr missense NM_001384523.1:c.1073A>C NP_001371452.1:p.Lys358Thr missense NM_001384524.1:c.1073A>C NP_001371453.1:p.Lys358Thr missense NM_001384525.1:c.1073A>C NP_001371454.1:p.Lys358Thr missense NM_001384526.1:c.1073A>C NP_001371455.1:p.Lys358Thr missense NM_001384527.1:c.1073A>C NP_001371456.1:p.Lys358Thr missense NM_001384529.1:c.1073A>C NP_001371458.1:p.Lys358Thr missense NM_001384530.1:c.1073A>C NP_001371459.1:p.Lys358Thr missense NM_001384531.1:c.1073A>C NP_001371460.1:p.Lys358Thr missense NM_001384532.1:c.1073A>C NP_001371461.1:p.Lys358Thr missense NM_001384533.1:c.1073A>C NP_001371462.1:p.Lys358Thr missense NM_001384534.1:c.1073A>C NP_001371463.1:p.Lys358Thr missense NM_001384535.1:c.1073A>C NP_001371464.1:p.Lys358Thr missense NM_001384536.1:c.1073A>C NP_001371465.1:p.Lys358Thr missense NM_001384537.1:c.1073A>C NP_001371466.1:p.Lys358Thr missense NM_001384538.1:c.1073A>C NP_001371467.1:p.Lys358Thr missense NM_001384539.1:c.983A>C NP_001371468.1:p.Lys328Thr missense NM_001384540.1:c.644A>C NP_001371469.1:p.Lys215Thr missense NM_001384541.1:c.644A>C NP_001371470.1:p.Lys215Thr missense NM_017660.5:c.1073A>C NP_060130.3:p.Lys358Thr missense NR_169268.1:n.1537A>C non-coding transcript variant NC_000019.10:g.19498591A>C NC_000019.9:g.19609400A>C - Protein change
- K215T, K328T, K358T
- Other names
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- Canonical SPDI
- NC_000019.10:19498590: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
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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
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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
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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 |
48 | 66 |
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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Jun 6, 2023 | RCV003994718.1 |
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
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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
(Jun 06, 2023)
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criteria provided, single submitter
Method: clinical testing
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Neurodevelopmental disorder
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
germline
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Molecular Genetics, Royal Melbourne Hospital
Additional submitter:
Shariant Australia, Australian Genomics
Accession: SCV004812728.1
First in ClinVar: Apr 15, 2024 Last updated: Apr 15, 2024 |
Comment:
This sequence change in GATAD2A is predicted to replace lysine with threonine at codon 358, p.(Lys358Thr). The lysine residue is highly conserved (99 vertebrates, UCSC), … (more)
This sequence change in GATAD2A is predicted to replace lysine with threonine at codon 358, p.(Lys358Thr). The lysine residue is highly conserved (99 vertebrates, UCSC), and is located in the CR2 domain (PMID: 31116477). There is a moderate physicochemical difference between lysine and threonine. This variant is absent from the population database gnomAD v2.1 and v3.1. To our knowledge, this variant is novel and has not been previously reported in the relevant scientific literature or databases. Computational evidence is uninformative for the missense substitution (REVEL = 0.5). Based on the classification scheme RMH Modified ACMG/AMP Guidelines v1.6.1, this variant is classified as a VARIANT OF UNCERTAIN SIGNIFICANCE. Following criteria are met: PM2_Supporting. (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
HelpTitle | Author | Journal | Year | Link |
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MetaDome: Pathogenicity analysis of genetic variants through aggregation of homologous human protein domains. | Wiel L | Human mutation | 2019 | PMID: 31116477 |
Text-mined citations for this variant ...
HelpRecord last updated Apr 20, 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.