NM_000310.4(PPT1):c.329A>G (p.Asn110Ser) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Sep 20, 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:: RCV000724058.9

Allele description [Variation Report for NM_000310.4(PPT1):c.329A>G (p.Asn110Ser)]

NM_000310.4(PPT1):c.329A>G (p.Asn110Ser)

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.329A>G (p.Asn110Ser)

Other names:

p.N110S:AAT>AGT

HGVS:

NC_000001.11:g.40092078T>C
NG_009192.1:g.10393A>G
NM_000310.4:c.329A>GMANE SELECT
NM_001142604.2:c.125-2566A>G
NM_001363695.2:c.329A>G
NP_000301.1:p.Asn110Ser
NP_000301.1:p.Asn110Ser
NP_001350624.1:p.Asn110Ser
LRG_690t1:c.329A>G
LRG_690:g.10393A>G
LRG_690p1:p.Asn110Ser
NC_000001.10:g.40557750T>C
NM_000310.3:c.329A>G

Protein change:

N110S

Links:

dbSNP: rs142894102

NCBI 1000 Genomes Browser:

rs142894102

Molecular consequence:

NM_001142604.2:c.125-2566A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_000310.4:c.329A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001363695.2:c.329A>G - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000228845	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Uncertain significance (Aug 22, 2014)	germline	clinical testing	Citation Link,
SCV000242336	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Sep 20, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000228845

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions 2015)

Uncertain significance
(Aug 22, 2014)

germline

clinical testing

Citation Link,

SCV000242336

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Sep 20, 2024)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	1	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Eurofins Ntd Llc (ga), SCV000228845.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		1	not provided	not provided	not provided

From GeneDx, SCV000242336.15

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Reported in the heterozygous state in a patient with cognitive impairment, ADHD, and epilepsy in the published literature; however, a second PPT1 variant was not identified (PMID: 33528079); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Observed in a homozygous state in a patient with episodic torticollis and sudden cardiac arrest who also harbored another homozygous variant in a gene related to the phenotype (PMID: 35693655); This variant is associated with the following publications: (PMID: 34426522, 35693655, 30541466, 33528079, Bhavsar2016[CaseReport])

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 8, 2024

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