NM_000466.3(PEX1):c.782_783del (p.Gln261fs) AND Inborn genetic diseases

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 23, 2023
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:: RCV003162722.2

Allele description [Variation Report for NM_000466.3(PEX1):c.782_783del (p.Gln261fs)]

NM_000466.3(PEX1):c.782_783del (p.Gln261fs)

Gene:

PEX1:peroxisomal biogenesis factor 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

7q21.2

Genomic location:

Preferred name:

NM_000466.3(PEX1):c.782_783del (p.Gln261fs)

HGVS:

NC_000007.14:g.92517732_92517733del
NG_008341.2:g.15799_15800del
NM_000466.3:c.782_783delMANE SELECT
NM_001282677.2:c.782_783del
NM_001282678.2:c.158_159del
NP_000457.1:p.Gln261fs
NP_001269606.1:p.Gln261fs
NP_001269607.1:p.Gln53fs
NC_000007.13:g.92147046_92147047del
NC_000007.13:g.92147046_92147047delTT
NG_008341.1:g.15799_15800del
NM_000466.2:c.782_783delAA

Protein change:

Q261fs

Links:

dbSNP: rs749067142

NCBI 1000 Genomes Browser:

rs749067142

Molecular consequence:

NM_000466.3:c.782_783del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001282677.2:c.782_783del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001282678.2:c.158_159del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003903720	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Pathogenic (Feb 23, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 2324705, 19105186, 23247051, 33708531 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003903720

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Pathogenic
(Feb 23, 2023)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

Citation Link

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

Nothing to display

See all PubMed Citations (4)

Details of each submission

From Ambry Genetics, SCV003903720.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

The c.782_783delAA (p.Q261Rfs*8) alteration, located in exon 5 (coding exon 5) of the PEX1 gene, consists of a deletion of 2 nucleotides from position 782 to 783, causing a translational frameshift with a predicted alternate stop codon after 8 amino acids. This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. Based on data from gnomAD, the c.782_783delAA allele has an overall frequency of 0.004% (9/249146) total alleles studied. The highest observed frequency was 0.013% (4/30214) of South Asian alleles. This variant has been reported compound heterozygous with other PEX1 variants in individuals with features consistent with PEX1-related peroxisome biogenesis spectrum disorder (Yik, 2009; Sun, 2013; Lu, 2021). Based on the available evidence, this alteration is classified as pathogenic.

#	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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