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NM_012463.4(ATP6V0A2):c.2229T>C (p.Cys743=)

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Interpretation:
Conflicting interpretations of pathogenicity​

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

Review status:
criteria provided, conflicting interpretations
Submissions:
6 (Most recent: Oct 1, 2021)
Last evaluated:
Sep 23, 2020
Accession:
VCV000194862.9
Variation ID:
194862
Description:
single nucleotide variant
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NM_012463.4(ATP6V0A2):c.2229T>C (p.Cys743=)

Allele ID
192025
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
12q24.31
Genomic location
12: 123754473 (GRCh38) GRCh38 UCSC
12: 124239020 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000012.11:g.124239020T>C
NC_000012.12:g.123754473T>C
NG_012743.1:g.47156T>C
NM_012463.4:c.2229T>C MANE Select NP_036595.2:p.Cys743= synonymous
Protein change
-
Other names
-
Canonical SPDI
NC_000012.12:123754472:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
0.00100 (C)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00114
The Genome Aggregation Database (gnomAD) 0.00073
1000 Genomes Project 0.00100
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00092
Links
ClinGen: CA241054
dbSNP: rs150508296
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Jun 14, 2016 RCV000364298.2
Benign 1 criteria provided, single submitter Dec 31, 2019 RCV001087624.1
Conflicting interpretations of pathogenicity 4 criteria provided, conflicting interpretations Sep 23, 2020 RCV000724863.7
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
ATP6V0A2 - - GRCh38
GRCh37
363 397

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
Cutis Laxa, Recessive
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000376941.2
Submitted: (Oct 18, 2016)
Evidence details
Uncertain significance
(May 22, 2015)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000226801.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Mar 28, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV001143084.1
Submitted: (Sep 25, 2019)
Evidence details
Benign
(Dec 31, 2019)
criteria provided, single submitter
Method: clinical testing
ALG9 congenital disorder of glycosylation
Allele origin: germline
Invitae
Accession: SCV001023381.2
Submitted: (Jan 29, 2020)
Evidence details
Likely benign
(Sep 23, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000527506.5
Submitted: (Oct 01, 2021)
Evidence details
Likely benign
(Aug 01, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001502155.3
Submitted: (Jul 04, 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=ATP6V0A2 - - - -

Text-mined citations for rs150508296...

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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 16, 2021