The c.1390A>G (p.R464G) alteration is located in exon 15 (coding exon 14) of the PAPD4 gene. This alteration results from a A to G substitution at nucleotide position 1390, causing the arginine (R) at amino acid position 464 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
ClinVar Genomic variation as it relates to human health
NM_001114394.3(TENT2):c.1390A>G (p.Arg464Gly)
Germline
Classification
Help
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.
(1)
Help
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.
Uncertain significance
1
criteria provided, single submitter
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_001114394.3(TENT2):c.1390A>G (p.Arg464Gly)
Variation ID: 2528118 Accession: VCV002528118.2
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 5q14.1 5: 79685208 (GRCh38) [ NCBI UCSC ] 5: 78981031 (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 Mar 22, 2023 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_001114394.3:c.1390A>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001107866.1:p.Arg464Gly missense NM_001114393.3:c.1390A>G NP_001107865.1:p.Arg464Gly missense NM_001297744.3:c.1378A>G NP_001284673.1:p.Arg460Gly missense NM_001297745.3:c.1261A>G NP_001284674.1:p.Arg421Gly missense NM_001349548.2:c.721A>G NP_001336477.1:p.Arg241Gly missense NM_001349549.2:c.1465A>G NP_001336478.1:p.Arg489Gly missense NM_001349550.2:c.1465A>G NP_001336479.1:p.Arg489Gly missense NM_001349551.2:c.1453A>G NP_001336480.1:p.Arg485Gly missense NM_001349552.2:c.1390A>G NP_001336481.1:p.Arg464Gly missense NM_001349553.2:c.1390A>G NP_001336482.1:p.Arg464Gly missense NM_001349554.2:c.1378A>G NP_001336483.1:p.Arg460Gly missense NM_001388093.1:c.1465A>G NP_001375022.1:p.Arg489Gly missense NM_001388094.1:c.1465A>G NP_001375023.1:p.Arg489Gly missense NM_001388095.1:c.1453A>G NP_001375024.1:p.Arg485Gly missense NM_001388096.1:c.1453A>G NP_001375025.1:p.Arg485Gly missense NM_001388097.1:c.1453A>G NP_001375026.1:p.Arg485Gly missense NM_001388098.1:c.1450A>G NP_001375027.1:p.Arg484Gly missense NM_001388099.1:c.1420A>G NP_001375028.1:p.Arg474Gly missense NM_001388100.1:c.1420A>G NP_001375029.1:p.Arg474Gly missense NM_001388101.1:c.1408A>G NP_001375030.1:p.Arg470Gly missense NM_001388102.1:c.1390A>G NP_001375031.1:p.Arg464Gly missense NM_001388103.1:c.1390A>G NP_001375032.1:p.Arg464Gly missense NM_001388105.1:c.1390A>G NP_001375034.1:p.Arg464Gly missense NM_001388106.1:c.1390A>G NP_001375035.1:p.Arg464Gly missense NM_001388107.1:c.1390A>G NP_001375036.1:p.Arg464Gly missense NM_001388108.1:c.1390A>G NP_001375037.1:p.Arg464Gly missense NM_001388109.1:c.1390A>G NP_001375038.1:p.Arg464Gly missense NM_001388110.1:c.1390A>G NP_001375039.1:p.Arg464Gly missense NM_001388111.1:c.1390A>G NP_001375040.1:p.Arg464Gly missense NM_001388112.1:c.1390A>G NP_001375041.1:p.Arg464Gly missense NM_001388113.1:c.1387A>G NP_001375042.1:p.Arg463Gly missense NM_001388114.1:c.1378A>G NP_001375043.1:p.Arg460Gly missense NM_001388115.1:c.1378A>G NP_001375044.1:p.Arg460Gly missense NM_001388116.1:c.1378A>G NP_001375045.1:p.Arg460Gly missense NM_001388117.1:c.1378A>G NP_001375046.1:p.Arg460Gly missense NM_001388118.1:c.1378A>G NP_001375047.1:p.Arg460Gly missense NM_001388119.1:c.1378A>G NP_001375048.1:p.Arg460Gly missense NM_001388120.1:c.1378A>G NP_001375049.1:p.Arg460Gly missense NM_001388121.1:c.1378A>G NP_001375050.1:p.Arg460Gly missense NM_001388122.1:c.1378A>G NP_001375051.1:p.Arg460Gly missense NM_001388123.1:c.1378A>G NP_001375052.1:p.Arg460Gly missense NM_001388124.1:c.1378A>G NP_001375053.1:p.Arg460Gly missense NM_001388125.1:c.1378A>G NP_001375054.1:p.Arg460Gly missense NM_001388126.1:c.1378A>G NP_001375055.1:p.Arg460Gly missense NM_001388127.1:c.1378A>G NP_001375056.1:p.Arg460Gly missense NM_001388128.1:c.1378A>G NP_001375057.1:p.Arg460Gly missense NM_001388129.1:c.1378A>G NP_001375058.1:p.Arg460Gly missense NM_001388130.1:c.1375A>G NP_001375059.1:p.Arg459Gly missense NM_001388131.1:c.1300A>G NP_001375060.1:p.Arg434Gly missense NM_001388132.1:c.1288A>G NP_001375061.1:p.Arg430Gly missense NM_001388133.1:c.1261A>G NP_001375062.1:p.Arg421Gly missense NM_001388134.1:c.1249A>G NP_001375063.1:p.Arg417Gly missense NM_001388135.1:c.1249A>G NP_001375064.1:p.Arg417Gly missense NM_001388136.1:c.1030A>G NP_001375065.1:p.Arg344Gly missense NM_001388137.1:c.796A>G NP_001375066.1:p.Arg266Gly missense NM_173797.5:c.1390A>G NP_776158.2:p.Arg464Gly missense NC_000005.10:g.79685208A>G NC_000005.9:g.78981031A>G - Protein change
- R459G, R241G, R421G, R460G, R470G, R266G, R430G, R463G, R474G, R485G, R489G, R344G, R417G, R434G, R464G, R484G
- Other names
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- Canonical SPDI
- NC_000005.10:79685207:A: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
Help
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
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
|---|---|---|---|---|---|---|
| HI score
Help
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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| TENT2 | - | - |
GRCh38 GRCh37 |
30 | 44 | |
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
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
|---|---|---|---|---|
| Uncertain significance (1) |
criteria provided, single submitter
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Mar 22, 2023 | RCV004303126.1 |
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
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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Uncertain significance
(Mar 22, 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: SCV003959525.2
First in ClinVar: Jul 08, 2023 Last updated: May 01, 2024 |
Comment:
The c.1390A>G (p.R464G) alteration is located in exon 15 (coding exon 14) of the PAPD4 gene. This alteration results from a A to G substitution … (more)
The c.1390A>G (p.R464G) alteration is located in exon 15 (coding exon 14) of the PAPD4 gene. This alteration results from a A to G substitution at nucleotide position 1390, causing the arginine (R) at amino acid position 464 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. (less)
|
Comment:
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. |
Comment:
The c.1390A>G (p.R464G) alteration is located in exon 15 (coding exon 14) of the PAPD4 gene. This alteration results from a A to G substitution at nucleotide position 1390, causing the arginine (R) at amino acid position 464 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
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 Nov 10, 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.