NM_003630.3(PEX3):c.991G>A (p.Gly331Arg) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 1, 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:: RCV001851064.6

Allele description [Variation Report for NM_003630.3(PEX3):c.991G>A (p.Gly331Arg)]

NM_003630.3(PEX3):c.991G>A (p.Gly331Arg)

Gene:

PEX3:peroxisomal biogenesis factor 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

6q24.2

Genomic location:

Preferred name:

NM_003630.3(PEX3):c.991G>A (p.Gly331Arg)

Other names:

NM_003630.2:c.991G>A(p.Gly331Arg)

HGVS:

NC_000006.12:g.143485201G>A
NG_008459.1:g.39421G>A
NM_003630.3:c.991G>AMANE SELECT
NP_003621.1:p.Gly331Arg
NC_000006.11:g.143806338G>A
NC_000006.11:g.143806338G>A
NM_003630.2:c.991G>A

Protein change:

G331R; GLY331ARG

Links:

OMIM: 603164.0004; dbSNP: rs1057523689

NCBI 1000 Genomes Browser:

rs1057523689

Molecular consequence:

NM_003630.3:c.991G>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
SCV002173599	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 1, 2021)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 27557811, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002173599

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 1, 2021)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Novel PEX3 Gene Mutations Resulting in a Moderate Zellweger Spectrum Disorder.

Maxit C, Denzler I, Marchione D, Agosta G, Koster J, Wanders RJA, Ferdinandusse S, Waterham HR.

JIMD Rep. 2017;34:71-75. doi: 10.1007/8904_2016_10. Epub 2016 Aug 25.

PubMed [citation]

PMID:: 27557811
PMCID:: PMC5509555

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002173599.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C15"). This variant has been observed in individual(s) with Zellweger spectrum disorder (PMID: 27557811). ClinVar contains an entry for this variant (Variation ID: 390240). This variant is not present in population databases (ExAC no frequency). This sequence change replaces glycine with arginine at codon 331 of the PEX3 protein (p.Gly331Arg). The glycine residue is highly conserved and there is a moderate physicochemical difference between glycine and arginine.

#	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		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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