ClinVar Genomic variation as it relates to human health
NM_001195248.2(APTX):c.513G>A (p.Leu171=)
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.
Uncertain significance(1); Benign(1); Likely benign(5)
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_001195248.2(APTX):c.513G>A (p.Leu171=)
Variation ID: 262911 Accession: VCV000262911.35
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 9p21.1 9: 32986001 (GRCh38) [ NCBI UCSC ] 9: 32985999 (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 Oct 3, 2016 Aug 4, 2024 Aug 4, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001195248.2:c.513G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001182177.2:p.Leu171= synonymous NM_001195249.2:c.513G>A NP_001182178.1:p.Leu171= synonymous NM_001195250.2:c.351G>A NP_001182179.2:p.Leu117= synonymous NM_001195251.2:c.513G>A NP_001182180.1:p.Leu171= synonymous NM_001195252.2:c.297G>A NP_001182181.2:p.Leu99= synonymous NM_001195254.2:c.351G>A NP_001182183.1:p.Leu117= synonymous NM_001368995.1:c.513G>A NP_001355924.1:p.Leu171= synonymous NM_001368996.1:c.513G>A NP_001355925.1:p.Leu171= synonymous NM_001368997.1:c.513G>A NP_001355926.1:p.Leu171= synonymous NM_001368998.1:c.513G>A NP_001355927.1:p.Leu171= synonymous NM_001368999.1:c.513G>A NP_001355928.1:p.Leu171= synonymous NM_001369000.1:c.351G>A NP_001355929.1:p.Leu117= synonymous NM_001369001.1:c.351G>A NP_001355930.1:p.Leu117= synonymous NM_001369002.1:c.249G>A NP_001355931.1:p.Leu83= synonymous NM_001369003.1:c.249G>A NP_001355932.1:p.Leu83= synonymous NM_001369004.1:c.249G>A NP_001355933.1:p.Leu83= synonymous NM_001369005.1:c.249G>A NP_001355934.1:p.Leu83= synonymous NM_001369006.1:c.249G>A NP_001355935.1:p.Leu83= synonymous NM_001370669.1:c.249G>A NP_001357598.1:p.Leu83= synonymous NM_001370670.1:c.249G>A NP_001357599.1:p.Leu83= synonymous NM_001370673.1:c.249G>A NP_001357602.1:p.Leu83= synonymous NM_175069.3:c.513G>A NP_778239.2:p.Leu171= synonymous NM_175073.3:c.513G>A NP_778243.1:p.Leu171= synonymous NR_036577.2:n.464G>A non-coding transcript variant NR_160920.1:n.579G>A non-coding transcript variant NR_160921.1:n.483G>A non-coding transcript variant NR_160922.1:n.714G>A non-coding transcript variant NR_160923.1:n.518G>A non-coding transcript variant NR_160924.1:n.523G>A non-coding transcript variant NR_160925.1:n.719G>A non-coding transcript variant NR_160926.1:n.509G>A non-coding transcript variant NR_160927.1:n.829G>A non-coding transcript variant NR_160928.1:n.719G>A non-coding transcript variant NR_160929.1:n.633G>A non-coding transcript variant NR_160930.1:n.459G>A non-coding transcript variant NR_160931.1:n.698G>A non-coding transcript variant NC_000009.12:g.32986001C>T NC_000009.11:g.32985999C>T NG_012821.2:g.44131G>A - Protein change
- Other names
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- Canonical SPDI
- NC_000009.12:32986000: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.
Exome Aggregation Consortium (ExAC) 0.00026
The Genome Aggregation Database (gnomAD), exomes 0.00031
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00054
The Genome Aggregation Database (gnomAD) 0.00063
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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APTX | - | - |
GRCh38 GRCh37 |
287 | 356 |
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. |
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Benign/Likely benign (2) |
criteria provided, multiple submitters, no conflicts
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Jun 4, 2015 | RCV000242502.8 | |
Likely benign (4) |
criteria provided, multiple submitters, no conflicts
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Aug 4, 2023 | RCV000755827.31 | |
Uncertain significance (1) |
criteria provided, single submitter
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Apr 27, 2017 | RCV001165625.5 |
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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Likely benign
(-)
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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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PreventionGenetics, part of Exact Sciences
Accession: SCV000316587.1
First in ClinVar: Oct 03, 2016 Last updated: Oct 03, 2016 |
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Benign
(Jun 04, 2015)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV000512093.4
First in ClinVar: Mar 08, 2017 Last updated: Mar 08, 2017 |
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. (less)
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Likely benign
(Jun 19, 2018)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: unknown
Allele origin:
germline
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ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV000883414.1
First in ClinVar: Feb 18, 2019 Last updated: Feb 18, 2019 |
Comment:
The c.513G>A variant (rs140888559; ClinVar Variation ID: 262911) has not been reported in the medical literature in association with disease. This variant does not alter … (more)
The c.513G>A variant (rs140888559; ClinVar Variation ID: 262911) has not been reported in the medical literature in association with disease. This variant does not alter amino acid sequence of APTX protein, affects a weakly conserved nucleotide, and computational analyses (Alamut v.2.11) predict that this variant does not alter splicing. This variant is rare in the general population and is found with an overall allele frequency of 0.03% (90/271,614 alleles) in the Genome Aggregation Database. Based on available information, this variant is considered to be likely benign. (less)
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Likely benign
(Apr 29, 2019)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Athena Diagnostics
Accession: SCV001143039.1
First in ClinVar: Jan 19, 2020 Last updated: Jan 19, 2020 |
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Uncertain significance
(Apr 27, 2017)
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criteria provided, single submitter
Method: clinical testing
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Ataxia, early-onset, with oculomotor apraxia and hypoalbuminemia
Affected status: unknown
Allele origin:
germline
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Illumina Laboratory Services, Illumina
Accession: SCV001327836.1
First in ClinVar: May 31, 2020 Last updated: May 31, 2020 |
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. (less)
Observation 1: Observation 2: |
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Likely benign
(Aug 04, 2023)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Invitae
Accession: SCV002485733.3
First in ClinVar: Apr 08, 2022 Last updated: Feb 14, 2024 |
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Likely benign
(Mar 01, 2023)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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CeGaT Center for Human Genetics Tuebingen
Accession: SCV002063230.18
First in ClinVar: Jan 29, 2022 Last updated: Aug 04, 2024 |
Comment:
APTX: BP4, BP7
Number of individuals with the variant: 3
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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 rs140888559 ...
HelpRecord last updated Aug 04, 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.