NM_000310.4(PPT1):c.3G>A (p.Met1Ile) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Mar 15, 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:: RCV002225282.2

Allele description [Variation Report for NM_000310.4(PPT1):c.3G>A (p.Met1Ile)]

NM_000310.4(PPT1):c.3G>A (p.Met1Ile)

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.3G>A (p.Met1Ile)

HGVS:

NC_000001.11:g.40097236C>T
NG_009192.1:g.5235G>A
NM_000310.4:c.3G>AMANE SELECT
NM_001142604.2:c.3G>A
NM_001363695.2:c.3G>A
NP_000301.1:p.Met1Ile
NP_000301.1:p.Met1Ile
NP_001136076.1:p.Met1Ile
NP_001350624.1:p.Met1Ile
LRG_690t1:c.3G>A
LRG_690:g.5235G>A
LRG_690p1:p.Met1Ile
NC_000001.10:g.40562908C>T
NM_000310.3:c.3G>A

Protein change:

M1I

Links:

dbSNP: rs386833645

NCBI 1000 Genomes Browser:

rs386833645

Molecular consequence:

NM_000310.4:c.3G>A - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001142604.2:c.3G>A - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001363695.2:c.3G>A - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_000310.4:c.3G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001142604.2:c.3G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001363695.2:c.3G>A - missense variant - [Sequence Ontology: SO:0001583]

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
SCV002504142	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely pathogenic (Mar 15, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002504142

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely pathogenic
(Mar 15, 2022)

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV002504142.3

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

Description

Published functional studies demonstrate a damaging effect suggesting a partial defect in protein expression (Lyly et al., 2007); Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 10191107, 33561134, 9664077, 17565660, 11440996, 29631617, 11073228)

#	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: Sep 29, 2024

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