ClinVar Genomic variation as it relates to human health
NM_172245.4(CSF2RA):c.610C>T (p.Gln204Ter)
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_172245.4(CSF2RA):c.610C>T (p.Gln204Ter)
Variation ID: 847249 Accession: VCV000847249.4
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: Xp22.33 Yp11.2 X: 1409366 (GRCh37) [ NCBI UCSC ] Y: 1359366 (GRCh37) [ NCBI UCSC ] X: 1290473 (GRCh38) [ NCBI UCSC ] Y: 1290473 (GRCh38) [ 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 May 16, 2022 May 28, 2022 May 4, 2022 - HGVS
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Nucleotide Protein Molecular
consequenceNM_172245.4:c.610C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_758448.1:p.Gln204Ter nonsense NM_001161529.2:c.610C>T NP_001155001.1:p.Gln204Ter nonsense NM_001161530.2:c.610C>T NP_001155002.1:p.Gln204Ter nonsense NM_001161531.2:c.610C>T NP_001155003.1:p.Gln204Ter nonsense NM_001161532.2:c.211C>T NP_001155004.1:p.Gln71Ter nonsense NM_001379153.1:c.610C>T NP_001366082.1:p.Gln204Ter nonsense NM_001379154.1:c.610C>T NP_001366083.1:p.Gln204Ter nonsense NM_001379155.1:c.610C>T NP_001366084.1:p.Gln204Ter nonsense NM_001379156.1:c.610C>T NP_001366085.1:p.Gln204Ter nonsense NM_001379158.1:c.610C>T NP_001366087.1:p.Gln204Ter nonsense NM_001379159.1:c.610C>T NP_001366088.1:p.Gln204Ter nonsense NM_001379160.1:c.610C>T NP_001366089.1:p.Gln204Ter nonsense NM_001379161.1:c.610C>T NP_001366090.1:p.Gln204Ter nonsense NM_001379162.1:c.610C>T NP_001366091.1:p.Gln204Ter nonsense NM_001379163.1:c.610C>T NP_001366092.1:p.Gln204Ter nonsense NM_001379164.1:c.610C>T NP_001366093.1:p.Gln204Ter nonsense NM_001379165.1:c.610C>T NP_001366094.1:p.Gln204Ter nonsense NM_001379166.1:c.610C>T NP_001366095.1:p.Gln204Ter nonsense NM_001379167.1:c.610C>T NP_001366096.1:p.Gln204Ter nonsense NM_001379168.1:c.610C>T NP_001366097.1:p.Gln204Ter nonsense NM_001379169.1:c.610C>T NP_001366098.1:p.Gln204Ter nonsense NM_006140.6:c.610C>T NP_006131.2:p.Gln204Ter nonsense NM_172246.4:c.610C>T NP_758449.1:p.Gln204Ter nonsense NM_172247.3:c.610C>T NP_758450.1:p.Gln204Ter nonsense NM_172249.4:c.610C>T NP_758452.1:p.Gln204Ter nonsense NR_027760.3:n.790C>T non-coding transcript variant NC_000023.11:g.1290473C>T NC_000024.10:g.1290473C>T NC_000023.10:g.1409366C>T NC_000024.9:g.1359366C>T NG_012280.1:g.26674C>T LRG_186:g.26674C>T - Protein change
- Q204*, Q71*
- Other names
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- Canonical SPDI
- NC_000024.10:1290472: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
Help
The frequency of the allele represented by this VCV record.
The Genome Aggregation Database (gnomAD) 0.00001
Trans-Omics for Precision Medicine (TOPMed) 0.00001
- 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
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
Help
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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CSF2RA |
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GRCh38 GRCh38 |
426 | 553 |
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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Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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May 4, 2022 | RCV001050755.5 |
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
Help
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
(May 15, 2019)
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criteria provided, single submitter
Method: clinical testing
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Surfactant metabolism dysfunction, pulmonary, 4
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV001214877.3
First in ClinVar: Apr 15, 2020 Last updated: May 16, 2022 |
Comment:
This sequence change creates a premature translational stop signal (p.Gln204*) in the CSF2RA gene. It is expected to result in an absent or disrupted protein … (more)
This sequence change creates a premature translational stop signal (p.Gln204*) in the CSF2RA gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with CSF2RA-related conditions. Loss-of-function variants in CSF2RA are known to be pathogenic (PMID: 20622029, 25425184). For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(May 04, 2022)
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criteria provided, single submitter
Method: clinical testing
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Surfactant metabolism dysfunction, pulmonary, 4
Affected status: unknown
Allele origin:
germline
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Mendelics
Accession: SCV002519452.1
First in ClinVar: May 28, 2022 Last updated: May 28, 2022 |
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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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Characterization of CSF2RA mutation related juvenile pulmonary alveolar proteinosis. | Hildebrandt J | Orphanet journal of rare diseases | 2014 | PMID: 25425184 |
Hereditary pulmonary alveolar proteinosis: pathogenesis, presentation, diagnosis, and therapy. | Suzuki T | American journal of respiratory and critical care medicine | 2010 | PMID: 20622029 |
Text-mined citations for rs2091299213 ...
HelpRecord last updated Sep 29, 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.