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NM_001195248.2(APTX):c.762G>A (p.Pro254=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(3);Likely benign(2);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
6 (Most recent: Sep 18, 2021)
Last evaluated:
Nov 10, 2020
Accession:
VCV000281340.7
Variation ID:
281340
Description:
single nucleotide variant
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NM_001195248.2(APTX):c.762G>A (p.Pro254=)

Allele ID
265577
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9p21.1
Genomic location
9: 32984639 (GRCh38) GRCh38 UCSC
9: 32984637 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_175073.2:c.762G>A NP_778243.1:p.Pro254= synonymous
NC_000009.11:g.32984637C>T
NC_000009.12:g.32984639C>T
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000009.12:32984638:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00040 (T)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00011
The Genome Aggregation Database (gnomAD) 0.00013
The Genome Aggregation Database (gnomAD), exomes 0.00084
1000 Genomes Project 0.00040
Exome Aggregation Consortium (ExAC) 0.00091
Links
ClinGen: CA5022332
dbSNP: rs571475924
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 3 criteria provided, multiple submitters, no conflicts Nov 10, 2020 RCV000710596.6
Likely benign 1 criteria provided, single submitter Jan 13, 2018 RCV000265858.2
Uncertain significance 1 criteria provided, single submitter Jun 14, 2016 RCV000302324.2
Benign 1 criteria provided, single submitter Jun 11, 2015 RCV000396031.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
APTX - - GRCh38
GRCh37
169 235

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
Coenzyme Q10 deficiency, Oculomotor Apraxia Type
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000479623.2
Submitted: (Oct 18, 2016)
Evidence details
Benign
(Jun 11, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000332087.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Ataxia-oculomotor apraxia type 1
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000479622.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Benign
(Sep 06, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000840839.1
Submitted: (Aug 31, 2018)
Evidence details
Benign
(Dec 31, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001059700.2
Submitted: (Jan 29, 2020)
Evidence details
Likely benign
(Nov 10, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001891816.1
Submitted: (Sep 18, 2021)
Evidence details

Functional evidence

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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 this variant

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Title Author Journal Year Link
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=APTX - - - -

Text-mined citations for rs571475924...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 24, 2021