ClinVar Genomic variation as it relates to human health
NM_017771.5(PXK):c.307A>T (p.Ile103Phe)
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.307A>T (p.Ile103Phe)
Variation ID: 2331129 Accession: VCV002331129.2
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 3p14.3 3: 58382619 (GRCh38) [ NCBI UCSC ] 3: 58368346 (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 Dec 1, 2022 - HGVS
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Nucleotide Protein Molecular
consequenceNM_017771.5:c.307A>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_060241.2:p.Ile103Phe missense NM_001289095.2:c.256A>T NP_001276024.1:p.Ile86Phe missense NM_001289096.2:c.208A>T NP_001276025.1:p.Ile70Phe missense NM_001289098.2:c.307A>T NP_001276027.1:p.Ile103Phe missense NM_001289099.2:c.58A>T NP_001276028.1:p.Ile20Phe missense NM_001289100.2:c.208A>T NP_001276029.1:p.Ile70Phe missense NM_001289101.2:c.-23-7963A>T intron variant NM_001349488.2:c.307A>T NP_001336417.1:p.Ile103Phe missense NM_001349489.2:c.58A>T NP_001336418.1:p.Ile20Phe missense NM_001349490.2:c.208A>T NP_001336419.1:p.Ile70Phe missense NM_001349491.2:c.-23-7963A>T intron variant NM_001349492.2:c.307A>T NP_001336421.1:p.Ile103Phe missense NM_001349493.2:c.307A>T NP_001336422.1:p.Ile103Phe missense NM_001349494.2:c.259A>T NP_001336423.1:p.Ile87Phe missense NM_001349495.2:c.259A>T NP_001336424.1:p.Ile87Phe missense NM_001349496.2:c.256A>T NP_001336425.1:p.Ile86Phe missense NM_001349497.2:c.256A>T NP_001336426.1:p.Ile86Phe missense NM_001349498.1:c.247A>T NP_001336427.1:p.Ile83Phe missense NM_001349499.2:c.307A>T NP_001336428.1:p.Ile103Phe missense NM_001349500.2:c.208A>T NP_001336429.1:p.Ile70Phe missense NM_001349501.2:c.259A>T NP_001336430.1:p.Ile87Phe missense NM_001349502.2:c.256A>T NP_001336431.1:p.Ile86Phe missense NM_001349503.2:c.307A>T NP_001336432.1:p.Ile103Phe missense NM_001349504.2:c.307A>T NP_001336433.1:p.Ile103Phe missense NM_001349506.2:c.307A>T NP_001336435.1:p.Ile103Phe missense NM_001349507.2:c.307A>T NP_001336436.1:p.Ile103Phe missense NM_001349508.2:c.307A>T NP_001336437.1:p.Ile103Phe missense NM_001349509.2:c.307A>T NP_001336438.1:p.Ile103Phe missense NM_001349510.2:c.259A>T NP_001336439.1:p.Ile87Phe missense NM_001349511.2:c.259A>T NP_001336440.1:p.Ile87Phe missense NM_001349512.2:c.259A>T NP_001336441.1:p.Ile87Phe missense NM_001349513.2:c.58A>T NP_001336442.1:p.Ile20Phe missense NM_001349514.2:c.256A>T NP_001336443.1:p.Ile86Phe missense NM_001349515.2:c.256A>T NP_001336444.1:p.Ile86Phe missense NM_001349516.2:c.259A>T NP_001336445.1:p.Ile87Phe missense NM_001349517.2:c.256A>T NP_001336446.1:p.Ile86Phe missense NM_001349518.2:c.256A>T NP_001336447.1:p.Ile86Phe missense NM_001349519.2:c.307A>T NP_001336448.1:p.Ile103Phe missense NM_001349520.2:c.307A>T NP_001336449.1:p.Ile103Phe missense NM_001349521.2:c.58A>T NP_001336450.1:p.Ile20Phe missense NM_001349522.2:c.208A>T NP_001336451.1:p.Ile70Phe missense NM_001349524.2:c.208A>T NP_001336453.1:p.Ile70Phe missense NM_001349525.2:c.-23-7963A>T intron variant NM_001349526.2:c.-23-7963A>T intron variant NM_001349527.2:c.307A>T NP_001336456.1:p.Ile103Phe missense NM_001349528.2:c.58A>T NP_001336457.1:p.Ile20Phe missense NM_001349529.2:c.58A>T NP_001336458.1:p.Ile20Phe missense NM_001349530.2:c.58A>T NP_001336459.1:p.Ile20Phe missense NM_001349531.2:c.58A>T NP_001336460.1:p.Ile20Phe missense NM_001349532.2:c.-23-7963A>T intron variant NM_001349533.2:c.-23-7963A>T intron variant NM_001349534.2:c.-23-7963A>T intron variant NM_001349535.2:c.-23-7963A>T intron variant NM_001349536.2:c.-23-7963A>T intron variant NM_001349537.2:c.-23-7963A>T intron variant NM_001349538.2:c.-23-7963A>T intron variant NM_001349539.2:c.-23-7963A>T intron variant NM_001349540.2:c.-23-7963A>T intron variant NR_146194.2:n.404A>T non-coding transcript variant NC_000003.12:g.58382619A>T NC_000003.11:g.58368346A>T - Protein change
- I83F, I70F, I103F, I86F, I87F, I20F
- Other names
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- Canonical SPDI
- NC_000003.12:58382618:A: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
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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 |
23 | 34 |
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
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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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Dec 1, 2022 | RCV004174793.1 |
Submissions - Germline
Classification
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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
(Dec 01, 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: SCV003671062.2
First in ClinVar: Feb 07, 2023 Last updated: May 01, 2024 |
Comment:
The c.307A>T (p.I103F) alteration is located in exon 4 (coding exon 4) of the PXK gene. This alteration results from a A to T substitution … (more)
The c.307A>T (p.I103F) alteration is located in exon 4 (coding exon 4) of the PXK gene. This alteration results from a A to T substitution at nucleotide position 307, causing the isoleucine (I) at amino acid position 103 to be replaced by a phenylalanine (F). 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 May 08, 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.