ClinVar Genomic variation as it relates to human health
NM_017771.5(PXK):c.1225T>G (p.Phe409Val)
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_017771.5(PXK):c.1225T>G (p.Phe409Val)
Variation ID: 2540654 Accession: VCV002540654.2
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 3p14.3 3: 58403905 (GRCh38) [ NCBI UCSC ] 3: 58389632 (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 Jul 8, 2023 May 1, 2024 Apr 25, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_017771.5:c.1225T>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_060241.2:p.Phe409Val missense NM_001289095.2:c.1174T>G NP_001276024.1:p.Phe392Val missense NM_001289096.2:c.1126T>G NP_001276025.1:p.Phe376Val missense NM_001289098.2:c.1225T>G NP_001276027.1:p.Phe409Val missense NM_001289099.2:c.976T>G NP_001276028.1:p.Phe326Val missense NM_001289100.2:c.1126T>G NP_001276029.1:p.Phe376Val missense NM_001289101.2:c.814T>G NP_001276030.1:p.Phe272Val missense NM_001349488.2:c.1225T>G NP_001336417.1:p.Phe409Val missense NM_001349489.2:c.976T>G NP_001336418.1:p.Phe326Val missense NM_001349490.2:c.1126T>G NP_001336419.1:p.Phe376Val missense NM_001349491.2:c.814T>G NP_001336420.1:p.Phe272Val missense NM_001349492.2:c.1225T>G NP_001336421.1:p.Phe409Val missense NM_001349493.2:c.1225T>G NP_001336422.1:p.Phe409Val missense NM_001349494.2:c.1177T>G NP_001336423.1:p.Phe393Val missense NM_001349495.2:c.1177T>G NP_001336424.1:p.Phe393Val missense NM_001349496.2:c.1174T>G NP_001336425.1:p.Phe392Val missense NM_001349497.2:c.1174T>G NP_001336426.1:p.Phe392Val missense NM_001349498.1:c.1165T>G NP_001336427.1:p.Phe389Val missense NM_001349499.2:c.1225T>G NP_001336428.1:p.Phe409Val missense NM_001349500.2:c.1126T>G NP_001336429.1:p.Phe376Val missense NM_001349501.2:c.1177T>G NP_001336430.1:p.Phe393Val missense NM_001349502.2:c.1174T>G NP_001336431.1:p.Phe392Val missense NM_001349503.2:c.1225T>G NP_001336432.1:p.Phe409Val missense NM_001349504.2:c.1225T>G NP_001336433.1:p.Phe409Val missense NM_001349506.2:c.1225T>G NP_001336435.1:p.Phe409Val missense NM_001349507.2:c.1225T>G NP_001336436.1:p.Phe409Val missense NM_001349508.2:c.1225T>G NP_001336437.1:p.Phe409Val missense NM_001349509.2:c.1225T>G NP_001336438.1:p.Phe409Val missense NM_001349510.2:c.1177T>G NP_001336439.1:p.Phe393Val missense NM_001349511.2:c.1177T>G NP_001336440.1:p.Phe393Val missense NM_001349512.2:c.1177T>G NP_001336441.1:p.Phe393Val missense NM_001349513.2:c.976T>G NP_001336442.1:p.Phe326Val missense NM_001349514.2:c.1174T>G NP_001336443.1:p.Phe392Val missense NM_001349515.2:c.1174T>G NP_001336444.1:p.Phe392Val missense NM_001349516.2:c.1177T>G NP_001336445.1:p.Phe393Val missense NM_001349517.2:c.1174T>G NP_001336446.1:p.Phe392Val missense NM_001349518.2:c.1174T>G NP_001336447.1:p.Phe392Val missense NM_001349519.2:c.1225T>G NP_001336448.1:p.Phe409Val missense NM_001349520.2:c.1225T>G NP_001336449.1:p.Phe409Val missense NM_001349521.2:c.976T>G NP_001336450.1:p.Phe326Val missense NM_001349522.2:c.1126T>G NP_001336451.1:p.Phe376Val missense NM_001349524.2:c.1126T>G NP_001336453.1:p.Phe376Val missense NM_001349525.2:c.814T>G NP_001336454.1:p.Phe272Val missense NM_001349526.2:c.814T>G NP_001336455.1:p.Phe272Val missense NM_001349527.2:c.1225T>G NP_001336456.1:p.Phe409Val missense NM_001349528.2:c.976T>G NP_001336457.1:p.Phe326Val missense NM_001349529.2:c.976T>G NP_001336458.1:p.Phe326Val missense NM_001349530.2:c.976T>G NP_001336459.1:p.Phe326Val missense NM_001349531.2:c.976T>G NP_001336460.1:p.Phe326Val missense NM_001349532.2:c.814T>G NP_001336461.1:p.Phe272Val missense NM_001349533.2:c.814T>G NP_001336462.1:p.Phe272Val missense NM_001349534.2:c.814T>G NP_001336463.1:p.Phe272Val missense NM_001349535.2:c.814T>G NP_001336464.1:p.Phe272Val missense NM_001349536.2:c.814T>G NP_001336465.1:p.Phe272Val missense NM_001349537.2:c.814T>G NP_001336466.1:p.Phe272Val missense NM_001349538.2:c.814T>G NP_001336467.1:p.Phe272Val missense NM_001349539.2:c.814T>G NP_001336468.1:p.Phe272Val missense NM_001349540.2:c.814T>G NP_001336469.1:p.Phe272Val missense NR_146193.2:n.1084T>G non-coding transcript variant NR_146194.2:n.1322T>G non-coding transcript variant NC_000003.12:g.58403905T>G NC_000003.11:g.58389632T>G - Protein change
- F272V, F389V, F409V, F326V, F376V, F393V, F392V
- Other names
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- Canonical SPDI
- NC_000003.12:58403904:T:G
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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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PXK | - | - |
GRCh38 GRCh37 |
30 | 42 |
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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Apr 25, 2023 | RCV004313769.1 |
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
(Apr 25, 2023)
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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: SCV003975672.2
First in ClinVar: Jul 08, 2023 Last updated: May 01, 2024 |
Comment:
The c.1225T>G (p.F409V) alteration is located in exon 13 (coding exon 13) of the PXK gene. This alteration results from a T to G substitution … (more)
The c.1225T>G (p.F409V) alteration is located in exon 13 (coding exon 13) of the PXK gene. This alteration results from a T to G substitution at nucleotide position 1225, causing the phenylalanine (F) at amino acid position 409 to be replaced by a valine (V). 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 Aug 11, 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.