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NM_000209.4(PDX1):c.719C>G (p.Pro240Arg) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 7, 2023
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV003727759.3

Allele description [Variation Report for NM_000209.4(PDX1):c.719C>G (p.Pro240Arg)]

NM_000209.4(PDX1):c.719C>G (p.Pro240Arg)

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.719C>G (p.Pro240Arg)
HGVS:
  • NC_000013.11:g.27924568C>G
  • NG_008183.1:g.9538C>G
  • NM_000209.4:c.719C>GMANE SELECT
  • NP_000200.1:p.Pro240Arg
  • NC_000013.10:g.28498705C>G
  • NM_000209.3:c.719C>G
  • p.PRO240ARG
Protein change:
P240R
Links:
dbSNP: rs753881947
NCBI 1000 Genomes Browser:
rs753881947
Molecular consequence:
  • NM_000209.4:c.719C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV004537107Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Aug 7, 2023)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Residual β cell function and monogenic variants in long-duration type 1 diabetes patients.

Yu MG, Keenan HA, Shah HS, Frodsham SG, Pober D, He Z, Wolfson EA, D'Eon S, Tinsley LJ, Bonner-Weir S, Pezzolesi MG, King GL.

J Clin Invest. 2019 Jul 2;129(8):3252-3263. doi: 10.1172/JCI127397.

PubMed [citation]
PMID:
31264968
PMCID:
PMC6668678

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004537107.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. ClinVar contains an entry for this variant (Variation ID: 447926). This missense change has been observed in individual(s) with type 1 diabetes (PMID: 31264968). This variant is present in population databases (no rsID available, gnomAD 0.006%). This sequence change replaces proline, which is neutral and non-polar, with arginine, which is basic and polar, at codon 240 of the PDX1 protein (p.Pro240Arg).

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

Last Updated: Nov 24, 2024