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NM_000209.4(PDX1):c.110A>T (p.Tyr37Phe) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Oct 2, 2022
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:
RCV002307649.1

Allele description [Variation Report for NM_000209.4(PDX1):c.110A>T (p.Tyr37Phe)]

NM_000209.4(PDX1):c.110A>T (p.Tyr37Phe)

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.110A>T (p.Tyr37Phe)
HGVS:
  • NC_000013.11:g.27920248A>T
  • NG_008183.1:g.5218A>T
  • NM_000209.4:c.110A>TMANE SELECT
  • NP_000200.1:p.Tyr37Phe
  • NC_000013.10:g.28494385A>T
  • NM_000209.3:c.110A>T
Protein change:
Y37F
Links:
dbSNP: rs1242190304
NCBI 1000 Genomes Browser:
rs1242190304
Molecular consequence:
  • NM_000209.4:c.110A>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002600368Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Uncertain significance
(Oct 2, 2022) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV002600368.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Variant summary: PDX1 c.110A>T (p.Tyr37Phe) results in a conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 7.3e-06 in 137784 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.110A>T in individuals affected with Familial Monogenic Diabetes (Maturity Onset Diabetes Of The Young 4)/Neonatal Diabetes Mellitus and no experimental evidence demonstrating its impact on protein function have been reported. One ClinVar submitter has assessed the variant since 2014: the variant was classified as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance.

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

Last Updated: May 7, 2024