NM_000466.3(PEX1):c.1239+1G>T AND Peroxisome biogenesis disorder 1A (Zellweger)

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Jan 31, 2020
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000633316.5

Allele description [Variation Report for NM_000466.3(PEX1):c.1239+1G>T]

NM_000466.3(PEX1):c.1239+1G>T

Gene:

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.1239+1G>T

HGVS:

NC_000007.14:g.92517275C>A
NG_008341.2:g.16257G>T
NM_000466.3:c.1239+1G>TMANE SELECT
NM_001282677.2:c.1239+1G>T
NM_001282678.2:c.615+1G>T
NC_000007.13:g.92146589C>A
NM_000466.2:c.1239+1G>T

Nucleotide change:

IVS5, G-T, +1

Links:

OMIM: 602136.0008; dbSNP: rs756876301

NCBI 1000 Genomes Browser:

rs756876301

Molecular consequence:

NM_000466.3:c.1239+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001282677.2:c.1239+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001282678.2:c.615+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]

Observations:

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000890871	Molecular Diagnostics Laboratory, M Health Fairview: University of Minnesota	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Nov 27, 2017)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 26387595, 19105186, 25741868
SCV001524805	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jan 31, 2020)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000890871

Molecular Diagnostics Laboratory, M Health Fairview: University of Minnesota

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Nov 27, 2017)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

SCV001524805

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jan 31, 2020)

unknown

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	1	not provided	not provided	1	not provided	clinical testing

Citations

PubMed

Heimler Syndrome Is Caused by Hypomorphic Mutations in the Peroxisome-Biogenesis Genes PEX1 and PEX6.

Ratbi I, Falkenberg KD, Sommen M, Al-Sheqaih N, Guaoua S, Vandeweyer G, Urquhart JE, Chandler KE, Williams SG, Roberts NA, El Alloussi M, Black GC, Ferdinandusse S, Ramdi H, Heimler A, Fryer A, Lynch SA, Cooper N, Ong KR, Smith CE, Inglehearn CF, Mighell AJ, et al.

Am J Hum Genet. 2015 Oct 1;97(4):535-45. doi: 10.1016/j.ajhg.2015.08.011. Epub 2015 Sep 17.

PubMed [citation]

PMID:: 26387595
PMCID:: PMC4596894

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

See all PubMed Citations (3)

Details of each submission

From Molecular Diagnostics Laboratory, M Health Fairview: University of Minnesota, SCV000890871.1

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

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

From Baylor Genetics, SCV001524805.1

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

Description

This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].

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

Last Updated: Nov 24, 2024

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