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NM_000310.4(PPT1):c.674T>C (p.Phe225Ser) AND not provided

Germline classification:
Likely pathogenic (2 submissions)
Last evaluated:
Feb 1, 2024
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV003328554.6

Allele description [Variation Report for NM_000310.4(PPT1):c.674T>C (p.Phe225Ser)]

NM_000310.4(PPT1):c.674T>C (p.Phe225Ser)

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.674T>C (p.Phe225Ser)
HGVS:
  • NC_000001.11:g.40078612A>G
  • NG_009192.1:g.23859T>C
  • NM_000310.4:c.674T>CMANE SELECT
  • NM_001142604.2:c.365T>C
  • NM_001363695.2:c.674T>C
  • NP_000301.1:p.Phe225Ser
  • NP_000301.1:p.Phe225Ser
  • NP_001136076.1:p.Phe122Ser
  • NP_001350624.1:p.Phe225Ser
  • LRG_690t1:c.674T>C
  • LRG_690:g.23859T>C
  • LRG_690p1:p.Phe225Ser
  • NC_000001.10:g.40544284A>G
  • NM_000310.3:c.674T>C
Protein change:
F122S
Links:
dbSNP: rs386833662
NCBI 1000 Genomes Browser:
rs386833662
Molecular consequence:
  • NM_000310.4:c.674T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001142604.2:c.365T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001363695.2:c.674T>C - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

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
SCV004035749GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Likely pathogenic
(Mar 13, 2023)
germlineclinical testing

Citation Link,

SCV004704131CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)
Likely pathogenic
(Feb 1, 2024)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV004035749.1

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

Description

In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 11589007, 11589012, 12125808, 14997939, 31741823, 34695666, Sangeeth_2019_Poster)

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

From CeGaT Center for Human Genetics Tuebingen, SCV004704131.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

PPT1: PM3:Strong, PM1, PM2, PP3

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

Last Updated: Jul 15, 2024