The c.1198A>G (p.T400A) alteration is located in exon 12 (coding exon 11) of the PAPD4 gene. This alteration results from a A to G substitution at nucleotide position 1198, causing the threonine (T) at amino acid position 400 to be replaced by an alanine (A). 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.1198A>G (p.Thr400Ala)
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)
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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.1198A>G (p.Thr400Ala)
Variation ID: 2476630 Accession: VCV002476630.2
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 5q14.1 5: 79669018 (GRCh38) [ NCBI UCSC ] 5: 78964841 (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 Apr 15, 2023 May 1, 2024 Jan 18, 2023 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_001114394.3:c.1198A>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001107866.1:p.Thr400Ala missense NM_001114393.3:c.1198A>G NP_001107865.1:p.Thr400Ala missense NM_001297744.3:c.1186A>G NP_001284673.1:p.Thr396Ala missense NM_001297745.3:c.1069A>G NP_001284674.1:p.Thr357Ala missense NM_001349548.2:c.529A>G NP_001336477.1:p.Thr177Ala missense NM_001349549.2:c.1273A>G NP_001336478.1:p.Thr425Ala missense NM_001349550.2:c.1273A>G NP_001336479.1:p.Thr425Ala missense NM_001349551.2:c.1261A>G NP_001336480.1:p.Thr421Ala missense NM_001349552.2:c.1198A>G NP_001336481.1:p.Thr400Ala missense NM_001349553.2:c.1198A>G NP_001336482.1:p.Thr400Ala missense NM_001349554.2:c.1186A>G NP_001336483.1:p.Thr396Ala missense NM_001388093.1:c.1273A>G NP_001375022.1:p.Thr425Ala missense NM_001388094.1:c.1273A>G NP_001375023.1:p.Thr425Ala missense NM_001388095.1:c.1261A>G NP_001375024.1:p.Thr421Ala missense NM_001388096.1:c.1261A>G NP_001375025.1:p.Thr421Ala missense NM_001388097.1:c.1261A>G NP_001375026.1:p.Thr421Ala missense NM_001388098.1:c.1258A>G NP_001375027.1:p.Thr420Ala missense NM_001388099.1:c.1228A>G NP_001375028.1:p.Thr410Ala missense NM_001388100.1:c.1228A>G NP_001375029.1:p.Thr410Ala missense NM_001388101.1:c.1216A>G NP_001375030.1:p.Thr406Ala missense NM_001388102.1:c.1198A>G NP_001375031.1:p.Thr400Ala missense NM_001388103.1:c.1198A>G NP_001375032.1:p.Thr400Ala missense NM_001388105.1:c.1198A>G NP_001375034.1:p.Thr400Ala missense NM_001388106.1:c.1198A>G NP_001375035.1:p.Thr400Ala missense NM_001388107.1:c.1198A>G NP_001375036.1:p.Thr400Ala missense NM_001388108.1:c.1198A>G NP_001375037.1:p.Thr400Ala missense NM_001388109.1:c.1198A>G NP_001375038.1:p.Thr400Ala missense NM_001388110.1:c.1198A>G NP_001375039.1:p.Thr400Ala missense NM_001388111.1:c.1198A>G NP_001375040.1:p.Thr400Ala missense NM_001388112.1:c.1198A>G NP_001375041.1:p.Thr400Ala missense NM_001388113.1:c.1195A>G NP_001375042.1:p.Thr399Ala missense NM_001388114.1:c.1186A>G NP_001375043.1:p.Thr396Ala missense NM_001388115.1:c.1186A>G NP_001375044.1:p.Thr396Ala missense NM_001388116.1:c.1186A>G NP_001375045.1:p.Thr396Ala missense NM_001388117.1:c.1186A>G NP_001375046.1:p.Thr396Ala missense NM_001388118.1:c.1186A>G NP_001375047.1:p.Thr396Ala missense NM_001388119.1:c.1186A>G NP_001375048.1:p.Thr396Ala missense NM_001388120.1:c.1186A>G NP_001375049.1:p.Thr396Ala missense NM_001388121.1:c.1186A>G NP_001375050.1:p.Thr396Ala missense NM_001388122.1:c.1186A>G NP_001375051.1:p.Thr396Ala missense NM_001388123.1:c.1186A>G NP_001375052.1:p.Thr396Ala missense NM_001388124.1:c.1186A>G NP_001375053.1:p.Thr396Ala missense NM_001388125.1:c.1186A>G NP_001375054.1:p.Thr396Ala missense NM_001388126.1:c.1186A>G NP_001375055.1:p.Thr396Ala missense NM_001388127.1:c.1186A>G NP_001375056.1:p.Thr396Ala missense NM_001388128.1:c.1186A>G NP_001375057.1:p.Thr396Ala missense NM_001388129.1:c.1186A>G NP_001375058.1:p.Thr396Ala missense NM_001388130.1:c.1183A>G NP_001375059.1:p.Thr395Ala missense NM_001388131.1:c.1108A>G NP_001375060.1:p.Thr370Ala missense NM_001388132.1:c.1096A>G NP_001375061.1:p.Thr366Ala missense NM_001388133.1:c.1069A>G NP_001375062.1:p.Thr357Ala missense NM_001388134.1:c.1057A>G NP_001375063.1:p.Thr353Ala missense NM_001388135.1:c.1057A>G NP_001375064.1:p.Thr353Ala missense NM_001388136.1:c.838A>G NP_001375065.1:p.Thr280Ala missense NM_001388137.1:c.604A>G NP_001375066.1:p.Thr202Ala missense NM_173797.5:c.1198A>G NP_776158.2:p.Thr400Ala missense NC_000005.10:g.79669018A>G NC_000005.9:g.78964841A>G - Protein change
- T177A, T366A, T396A, T425A, T357A, T399A, T410A, T420A, T202A, T280A, T370A, T395A, T400A, T406A, T421A, T353A
- Other names
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- Canonical SPDI
- NC_000005.10:79669017: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 | ||
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| 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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Jan 18, 2023 | RCV004265191.1 |
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
(Jan 18, 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: SCV003892620.2
First in ClinVar: Apr 15, 2023 Last updated: May 01, 2024 |
Comment:
The c.1198A>G (p.T400A) alteration is located in exon 12 (coding exon 11) of the PAPD4 gene. This alteration results from a A to G substitution … (more)
The c.1198A>G (p.T400A) alteration is located in exon 12 (coding exon 11) of the PAPD4 gene. This alteration results from a A to G substitution at nucleotide position 1198, causing the threonine (T) at amino acid position 400 to be replaced by an alanine (A). 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.1198A>G (p.T400A) alteration is located in exon 12 (coding exon 11) of the PAPD4 gene. This alteration results from a A to G substitution at nucleotide position 1198, causing the threonine (T) at amino acid position 400 to be replaced by an alanine (A). 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.