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NM_003620.4(PPM1D):c.1349T>G (p.Leu450Ter) AND Intellectual developmental disorder with gastrointestinal difficulties and high pain threshold

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Nov 3, 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:
RCV002308503.1

Allele description [Variation Report for NM_003620.4(PPM1D):c.1349T>G (p.Leu450Ter)]

NM_003620.4(PPM1D):c.1349T>G (p.Leu450Ter)

Gene:
PPM1D:protein phosphatase, Mg2+/Mn2+ dependent 1D [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17q23.2
Genomic location:
Preferred name:
NM_003620.4(PPM1D):c.1349T>G (p.Leu450Ter)
HGVS:
  • NC_000017.11:g.60663083T>G
  • NG_023265.1:g.67891T>G
  • NM_003620.4:c.1349T>GMANE SELECT
  • NP_003611.1:p.Leu450Ter
  • NP_003611.1:p.Leu450Ter
  • LRG_770t1:c.1349T>G
  • LRG_770:g.67891T>G
  • LRG_770p1:p.Leu450Ter
  • NC_000017.10:g.58740444T>G
  • NM_003620.3:c.1349T>G
Protein change:
L450*
Molecular consequence:
  • NM_003620.4:c.1349T>G - nonsense - [Sequence Ontology: SO:0001587]
Observations:
1

Condition(s)

Name:
Intellectual developmental disorder with gastrointestinal difficulties and high pain threshold (JDVS)
Synonyms:
JANSEN-DE VRIES SYNDROME
Identifiers:
MONDO: MONDO:0044318; MedGen: C4479517; OMIM: 617450

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002600254DASA
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Nov 3, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From DASA, SCV002600254.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

The c.1349T>G;p.(Leu450*) variant creates a premature translational stop signal in the PPM1D gene. It is expected to result in an absent or disrupted protein product - PVS1. The variant is present at low allele frequencies population databases (rs1163049039 – gnomAD 0.00006570%; ABraOM no frequency - https://abraom.ib.usp.br/) - PM2_supporting. In summary, the currently available evidence indicates that the variant is likely pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Feb 14, 2024