NM_000466.3(PEX1):c.2926+1G>A AND multiple conditions

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Nov 10, 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:: RCV001810430.10

Allele description [Variation Report for NM_000466.3(PEX1):c.2926+1G>A]

NM_000466.3(PEX1):c.2926+1G>A

Genes:

GATAD1:GATA zinc finger domain containing 1 [Gene - OMIM - HGNC]
PEX1:peroxisomal biogenesis factor 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7q21.2

Genomic location:

Preferred name:

NM_000466.3(PEX1):c.2926+1G>A

HGVS:

NC_000007.14:g.92494486C>T
NG_008341.2:g.39046G>A
NM_000466.3:c.2926+1G>AMANE SELECT
NM_001282677.2:c.2755+1G>A
NM_001282678.2:c.2302+1G>A
NC_000007.13:g.92123800C>T
NM_000466.2:c.2926+1G>A

Links:

dbSNP: rs267608179

NCBI 1000 Genomes Browser:

rs267608179

Molecular consequence:

NM_000466.3:c.2926+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001282677.2:c.2755+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001282678.2:c.2302+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:: Peroxisome biogenesis disorder 1A (Zellweger) (PBD1A)
Synonyms:: Zellweger leukodystrophy; Peroxisome biogenesis disorder 1a
Identifiers:: MONDO: MONDO:0008953; MedGen: C4721541; OMIM: 214100

Name:: Peroxisome biogenesis disorder 1B (PBD1B)
Synonyms:: Refsum disease, infantile form; Infantile Refsum disease; Infantile form of phytanic acid storage disease
Identifiers:: MONDO: MONDO:0011101; MedGen: C0282527; Orphanet: 44; OMIM: 601539

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002060375	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2021))	Likely pathogenic (Nov 10, 2021)	unknown	clinical testing	PubMed (3) [See all records that cite these PMIDs] 19105186, 15542397, 9398847 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002060375

Myriad Genetics, Inc.

criteria provided, single submitter

(Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2021))

Likely pathogenic
(Nov 10, 2021)

unknown

clinical testing

PubMed (3)
[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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Identification of novel mutations and sequence variation in the Zellweger syndrome spectrum of peroxisome biogenesis disorders.

Yik WY, Steinberg SJ, Moser AB, Moser HW, Hacia JG.

Hum Mutat. 2009 Mar;30(3):E467-80. doi: 10.1002/humu.20932.

PubMed [citation]

PMID:: 19105186
PMCID:: PMC2649967

The PEX Gene Screen: molecular diagnosis of peroxisome biogenesis disorders in the Zellweger syndrome spectrum.

Steinberg S, Chen L, Wei L, Moser A, Moser H, Cutting G, Braverman N.

Mol Genet Metab. 2004 Nov;83(3):252-63.

PubMed [citation]

PMID:: 15542397

See all PubMed Citations (3)

Details of each submission

From Myriad Genetics, Inc., SCV002060375.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

NM_000466.2(PEX1):c.2926+1G>A is a canonical splice variant classified as likely pathogenic in the context of peroxisome biogenesis disorder type 1. c.2926+1G>A has been observed in cases with relevant disease (PMID: 19105186, 15542397). Functional assessments of this variant are available in the literature (PMID: 9398847). c.2926+1G>A has been observed in population frequency databases (gnomAD NFE 0.004%). In summary, NM_000466.2(PEX1):c.2926+1G>A is a canonical splice variant in a gene where loss of function is a known mechanism of disease, is predicted to disrupt protein function, and has been observed more frequently in cases with the relevant disease than in healthy populations. Please note: this variant was assessed in the context of healthy population screening.

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

Last Updated: Nov 3, 2024

ClinVar

Relating variation to medicine