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NM_000310.4(PPT1):c.3G>A (p.Met1Ile) AND Inborn genetic diseases

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Mar 8, 2021
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:
RCV002514251.2

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)

Name:
Inborn genetic diseases
Identifiers:
MeSH: D030342; MedGen: C0950123

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV003558889Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)
Pathogenic
(Mar 8, 2021)
germlineclinical testing

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

Citation Link

Summary from all submissions

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

Citations

PubMed

Molecular genetics of palmitoyl-protein thioesterase deficiency in the U.S.

Das AK, Becerra CH, Yi W, Lu JY, Siakotos AN, Wisniewski KE, Hofmann SL.

J Clin Invest. 1998 Jul 15;102(2):361-70.

PubMed [citation]
PMID:
9664077
PMCID:
PMC508894

Details of each submission

From Ambry Genetics, SCV003558889.3

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

Description

The c.3G>A (p.M1?) alteration is located in coding exon 1 of the PPT1 gene and results from a G to A substitution at nucleotide position 1. This alters the methionine residue at the initiation codon (ATG). Sequence variations that modify the initiation codon are expected to result in either loss of translation initiation, N-terminal truncation, or cause a shift in the mRNA reading frame. This mutation was identified in two individuals with neuronal ceroid lipofuscinosis in conjunction with a second PPT1 variant (Das, 1998). Based on the available evidence, this alteration is classified as pathogenic.

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

Last Updated: Sep 29, 2024