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NM_000209.4(PDX1):c.716C>A (p.Pro239Gln)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
6 (Most recent: Sep 9, 2021)
Last evaluated:
Oct 1, 2019
Accession:
VCV000129881.8
Variation ID:
129881
Description:
single nucleotide variant
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NM_000209.4(PDX1):c.716C>A (p.Pro239Gln)

Allele ID
135327
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
13q12.2
Genomic location
13: 27924565 (GRCh38) GRCh38 UCSC
13: 28498702 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000013.10:g.28498702C>A
NC_000013.11:g.27924565C>A
NG_008183.1:g.9535C>A
NM_000209.4:c.716C>A MANE Select NP_000200.1:p.Pro239Gln missense
Protein change
P239Q
Other names
-
Canonical SPDI
NC_000013.11:27924564:C:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00639 (A)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.01048
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00562
1000 Genomes Project 0.00639
Trans-Omics for Precision Medicine (TOPMed) 0.00974
The Genome Aggregation Database (gnomAD) 0.00993
The Genome Aggregation Database (gnomAD) 0.01004
Trans-Omics for Precision Medicine (TOPMed) 0.01035
Links
ClinGen: CA231372
dbSNP: rs199644078
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 2 criteria provided, multiple submitters, no conflicts Jan 10, 2019 RCV000117899.4
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Oct 1, 2019 RCV000515153.3
Benign 1 criteria provided, single submitter Aug 14, 2018 RCV000445403.3
Likely benign 1 criteria provided, single submitter May 28, 2019 RCV000988972.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PDX1 - - GRCh38
GRCh37
71 102

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Mar 29, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Genetic Services Laboratory,University of Chicago
Accession: SCV000152173.2
Submitted: (Oct 04, 2017)
Evidence details
Likely benign
(Feb 27, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics
Accession: SCV000610490.1
Submitted: (Oct 05, 2017)
Evidence details
Likely benign
(May 28, 2019)
criteria provided, single submitter
Method: clinical testing
Maturity-onset diabetes of the young type 4
Allele origin: unknown
Mendelics
Accession: SCV001138927.1
Submitted: (Oct 22, 2019)
Evidence details
Benign
(Aug 14, 2018)
criteria provided, single submitter
Method: research
Monogenic diabetes
Allele origin: unknown
Personalized Diabetes Medicine Program,University of Maryland School of Medicine
Accession: SCV000537094.2
Submitted: (Feb 19, 2020)
Evidence details
Comment:
ACMG criteria: BA1 (2.8% in gnomAD African)= benign (REVEL score 0.221 + PP3 (3 predictors) + BP4 (8 predictors)= conflicting evidence, not using)
Benign
(Oct 01, 2019)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: unknown
Athena Diagnostics Inc
Accession: SCV001476619.1
Submitted: (Dec 30, 2020)
Evidence details
Publications
PubMed (5)
Benign
(Jan 10, 2019)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001847059.1
Submitted: (Sep 09, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 11270685, 27884173, 24097065)

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
- - - - PMID: 11270685
- - - - PMID: 11772903
- - - - PMID: 11978663
- - - - PMID: 19228875
- - - - PMID: 24097065

Text-mined citations for rs199644078...

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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 Nov 27, 2021