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NM_000310.4(PPT1):c.325T>G (p.Tyr109Asp) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Feb 11, 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:
RCV000188711.3

Allele description [Variation Report for NM_000310.4(PPT1):c.325T>G (p.Tyr109Asp)]

NM_000310.4(PPT1):c.325T>G (p.Tyr109Asp)

Gene:
PPT1:palmitoyl-protein thioesterase 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p34.2
Genomic location:
Preferred name:
NM_000310.4(PPT1):c.325T>G (p.Tyr109Asp)
Other names:
p.Y109D:TAC>GAC
HGVS:
  • NC_000001.11:g.40092082A>C
  • NG_009192.1:g.10389T>G
  • NM_000310.4:c.325T>GMANE SELECT
  • NM_001142604.2:c.125-2570T>G
  • NM_001363695.2:c.325T>G
  • NP_000301.1:p.Tyr109Asp
  • NP_000301.1:p.Tyr109Asp
  • NP_001350624.1:p.Tyr109Asp
  • LRG_690t1:c.325T>G
  • LRG_690:g.10389T>G
  • LRG_690p1:p.Tyr109Asp
  • NC_000001.10:g.40557754A>C
  • NM_000310.3:c.325T>G
  • P50897:p.Tyr109Asp
Protein change:
Y109D
Links:
UniProtKB: P50897#VAR_005552; dbSNP: rs386833642
NCBI 1000 Genomes Browser:
rs386833642
Molecular consequence:
  • NM_001142604.2:c.125-2570T>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000310.4:c.325T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001363695.2:c.325T>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000242335GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)		Pathogenic
(Feb 11, 2022) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000242335.13

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

Description

Published functional studies demonstrate a damaging effect with significantly impaired enzyme activity (Das et al., 2001); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 17565660, 10191107, 21990111, 11440996, 9664077, 11073228, 15719035)

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

Last Updated: Sep 29, 2024