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NM_016953.4(PDE11A):c.919C>T (p.Arg307Ter)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(2);Pathogenic(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Mar 14, 2019)
Last evaluated:
Mar 4, 2019
Accession:
VCV000005286.2
Variation ID:
5286
Description:
single nucleotide variant
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NM_016953.4(PDE11A):c.919C>T (p.Arg307Ter)

Allele ID
20325
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q31.2
Genomic location
2: 178014454 (GRCh38) GRCh38 UCSC
2: 178879181 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.178879181G>A
NC_000002.12:g.178014454G>A
NM_001077197.1:c.169C>T NP_001070665.1:p.Arg57Ter nonsense
... more HGVS
Protein change
R307*
Other names
-
Functional consequence
-
Global minor allele frequency (GMAF)
0.00180 (A)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00288
Trans-Omics for Precision Medicine (TOPMed) 0.00311
The Genome Aggregation Database (gnomAD) 0.00408
1000 Genomes Project 0.00180
Exome Aggregation Consortium (ExAC) 0.00304
Links
OMIM: 604961.0001
dbSNP: rs76308115
ClinGen: CA117375
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 2 criteria provided, single submitter Dec 3, 2017 RCV000005604.3
Likely benign 1 criteria provided, single submitter Jul 19, 2016 RCV000434464.1
Likely benign 1 criteria provided, single submitter Mar 4, 2019 RCV000950090.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PDE11A - - GRCh38
GRCh37
61 107

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Jul 19, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000514083.4
Submitted: (Mar 26, 2018)
Evidence details
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)
Pathogenic
(Dec 03, 2017)
criteria provided, single submitter
Method: clinical testing
Pigmented nodular adrenocortical disease, primary, 2
Allele origin: inherited
Genomic Research Center, Shahid Beheshti University of Medical Sciences
Accession: SCV000746542.1
Submitted: (Dec 03, 2017)
Evidence details
Likely benign
(Mar 04, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001096371.1
Submitted: (Mar 14, 2019)
Evidence details
Pathogenic
(Jul 01, 2006)
no assertion criteria provided
Method: literature only
PIGMENTED NODULAR ADRENOCORTICAL DISEASE, PRIMARY, 2
Allele origin: germline
OMIM
Accession: SCV000025786.2
Submitted: (Dec 30, 2010)
Evidence details
Publications
PubMed (1)

Citations for this variant

Title Author Journal Year Link
A genome-wide scan identifies mutations in the gene encoding phosphodiesterase 11A4 (PDE11A) in individuals with adrenocortical hyperplasia. Horvath A Nature genetics 2006 PMID: 16767104

Record last updated Dec 17, 2019