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NM_000209.4(PDX1):c.492G>T (p.Glu164Asp) AND Pancreatic agenesis 1

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Sep 1, 2003
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000020215.15

Allele description [Variation Report for NM_000209.4(PDX1):c.492G>T (p.Glu164Asp)]

NM_000209.4(PDX1):c.492G>T (p.Glu164Asp)

Gene:
PDX1:pancreatic and duodenal homeobox 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
13q12.2
Genomic location:
Preferred name:
NM_000209.4(PDX1):c.492G>T (p.Glu164Asp)
HGVS:
  • NC_000013.11:g.27924341G>T
  • NG_008183.1:g.9311G>T
  • NM_000209.4:c.492G>TMANE SELECT
  • NP_000200.1:p.Glu164Asp
  • NC_000013.10:g.28498478G>T
  • NM_000209.2:c.492G>T
Protein change:
E164D; GLU164ASP
Links:
OMIM: 600733.0008; dbSNP: rs80356661
NCBI 1000 Genomes Browser:
rs80356661
Molecular consequence:
  • NM_000209.4:c.492G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Pancreatic agenesis 1 (PAGEN1)
Synonyms:
PANCREATIC HYPOPLASIA, CONGENITAL; Pancreatic agenesis, congenital
Identifiers:
MONDO: MONDO:0024547; MedGen: C3891828; Orphanet: 2805; OMIM: 260370

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000029632OMIM
no assertion criteria provided
Pathogenic
(Sep 1, 2003)
germlineliterature only

PubMed (1)
[See all records that cite this PMID]

SCV000040552GeneReviews
no classification provided
not providedunknownliterature only

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownnot providednot providednot providednot providednot providednot providedliterature only
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Agenesis of human pancreas due to decreased half-life of insulin promoter factor 1.

Schwitzgebel VM, Mamin A, Brun T, Ritz-Laser B, Zaiko M, Maret A, Jornayvaz FR, Theintz GE, Michielin O, Melloul D, Philippe J.

J Clin Endocrinol Metab. 2003 Sep;88(9):4398-406.

PubMed [citation]
PMID:
12970316

Permanent Neonatal Diabetes Mellitus.

De León DD, Stanley CA.

2008 Feb 8 [updated 2016 Jul 29]. In: Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE, Amemiya A, editors. GeneReviews(®) [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2024.

PubMed [citation]
PMID:
20301620

Details of each submission

From OMIM, SCV000029632.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

In a female infant with pancreatic agenesis (PAGEN1; 260370), Schwitzgebel et al. (2003) identified compound heterozygosity for 2 missense mutations in exon 2 of the IPF1 gene: a 319G-T transversion resulting in a glu164-to-asp (E164D) substitution, and a 359G-A transition resulting in a glu178-to-lys (E178K; 600733.0009) substitution, both at highly conserved residues within helices 1 and 2, respectively, of the homeodomain. Her parents, who had high normal fasting glucose levels but no glucose intolerance, were each heterozygous for 1 of the mutations; a maternal uncle who had type 2 diabetes (T2D; 125853) was heterozygous for E164D. Both mutants decreased the protein half-life significantly, leading to intracellular IPF1 levels of 36% and 27% of wildtype levels. Both mutant proteins were translocated normally to the nucleus, and their DNA-binding activity on different known target promoters was similar to that of wildtype protein. However, transcriptional activity of both mutant IPF1 proteins, alone or in combination with FOXA2 (600288), PBX1 (176310), or the heterodimer E47-beta-2 (see 147141) was reduced, findings accounted for by decreased IPF1 steady-state levels and not by impaired protein-protein interactions. The authors concluded that IPF1 level is critical for human pancreas formation.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From GeneReviews, SCV000040552.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownnot providednot providednot providedAssert pathogenicitynot providednot providednot providednot provided

Last Updated: Nov 3, 2024