ClinVar Genomic variation as it relates to human health
NM_014489.4(PGAP2):c.609C>T (p.His203=)
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_014489.4(PGAP2):c.609C>T (p.His203=)
Variation ID: 2712857 Accession: VCV002712857.1
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 11p15.4 11: 3824277 (GRCh38) [ NCBI UCSC ] 11: 3845507 (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 Mar 29, 2023 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_014489.4:c.609C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_055304.1:p.His203= synonymous NM_001145438.2:c.597C>T NP_001138910.1:p.His199= synonymous NM_001145439.1:c.286C>T NP_001138911.1:p.Arg96Ter nonsense NM_001256235.1:c.480C>T NP_001243164.1:p.His160= synonymous NM_001256236.1:c.780C>T NP_001243165.1:p.His260= synonymous NM_001256237.1:c.597C>T NP_001243166.1:p.His199= synonymous NM_001256238.1:c.426C>T NP_001243167.1:p.His142= synonymous NM_001256239.2:c.426C>T NP_001243168.1:p.His142= synonymous NM_001256240.2:c.426C>T NP_001243169.1:p.His142= synonymous NM_001283038.1:c.597C>T NP_001269967.1:p.His199= synonymous NM_001283039.1:c.550C>T NP_001269968.1:p.Arg184Ter nonsense NM_001283040.1:c.169C>T NP_001269969.1:p.Arg57Ter nonsense NM_001346397.2:c.579C>T NP_001333326.1:p.His193= synonymous NM_001346398.2:c.426C>T NP_001333327.1:p.His142= synonymous NM_001346399.2:c.436C>T NP_001333328.1:p.Arg146Ter nonsense NM_001346400.2:c.426C>T NP_001333329.1:p.His142= synonymous NM_001346401.2:c.436C>T NP_001333330.1:p.Arg146Ter nonsense NM_001346402.2:c.546C>T NP_001333331.1:p.His182= synonymous NM_001346403.1:c.609C>T NP_001333332.1:p.His203= synonymous NM_001346404.1:c.426C>T NP_001333333.1:p.His142= synonymous NM_001346405.1:c.426C>T NP_001333334.1:p.His142= synonymous NR_027014.1:n.563C>T NR_027015.1:n.722C>T NR_027016.3:n.353C>T non-coding transcript variant NR_027017.4:n.746C>T non-coding transcript variant NR_027018.2:n.574C>T non-coding transcript variant NR_045923.2:n.368C>T non-coding transcript variant NR_045925.2:n.290C>T non-coding transcript variant NR_045926.2:n.290C>T non-coding transcript variant NR_045927.2:n.368C>T non-coding transcript variant NR_045929.2:n.481C>T non-coding transcript variant NR_104270.2:n.368C>T non-coding transcript variant NR_104271.2:n.628C>T non-coding transcript variant NR_104272.2:n.353C>T non-coding transcript variant NR_144427.2:n.368C>T non-coding transcript variant NR_144428.2:n.613C>T non-coding transcript variant NR_144429.2:n.353C>T non-coding transcript variant NR_144430.2:n.100C>T non-coding transcript variant NC_000011.10:g.3824277C>T NC_000011.9:g.3845507C>T NG_051812.1:g.31554C>T - Protein change
- R184*, R96*, R146*, R57*
- Other names
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- Canonical SPDI
- NC_000011.10:3824276: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
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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
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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| PGAP2 | - | - |
GRCh38 GRCh37 |
100 | 131 | |
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. |
|---|---|---|---|---|
| Benign (1) |
criteria provided, single submitter
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Mar 29, 2023 | RCV003548163.2 |
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
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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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Benign
(Mar 29, 2023)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV004267850.1
First in ClinVar: Feb 14, 2024 Last updated: Feb 14, 2024 |
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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
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.