NM_000287.4(PEX6):c.872_873del (p.Leu291fs) AND Peroxisome biogenesis disorder 4A (Zellweger)

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Dec 17, 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:: RCV002310077.2

Allele description [Variation Report for NM_000287.4(PEX6):c.872_873del (p.Leu291fs)]

NM_000287.4(PEX6):c.872_873del (p.Leu291fs)

Gene:

PEX6:peroxisomal biogenesis factor 6 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

6p21.1

Genomic location:

Preferred name:

NM_000287.4(PEX6):c.872_873del (p.Leu291fs)

HGVS:

NC_000006.12:g.42978279_42978280del
NG_008370.1:g.5965_5966del
NM_000287.4:c.872_873delMANE SELECT
NM_001316313.2:c.618+254_618+255del
NP_000278.3:p.Leu291fs
NC_000006.11:g.42946017_42946018del
NR_133009.2:n.903_904del

Protein change:

L291fs

Molecular consequence:

NM_000287.4:c.872_873del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001316313.2:c.618+254_618+255del - intron variant - [Sequence Ontology: SO:0001627]
NR_133009.2:n.903_904del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Peroxisome biogenesis disorder 4A (Zellweger) (PBD4A)
Synonyms:: Zellweger syndrome spectrum (PEX6-related)
Identifiers:: MONDO: MONDO:0013930; MedGen: C3553936; Orphanet: 912; OMIM: 614862

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002604836	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2021))	Likely pathogenic (Dec 17, 2021)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002604836

Myriad Genetics, Inc.

criteria provided, single submitter

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

Likely pathogenic
(Dec 17, 2021)

unknown

clinical testing

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

Details of each submission

From Myriad Genetics, Inc., SCV002604836.2

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

Description

NM_000287.3(PEX6):c.872_873delTC(L291Qfs*13) is expected to be pathogenic in the context of peroxisome biogenesis disorder type 4. This variant is predicted to lead to an abnormal or absent protein product due to the creation of a premature termination codon in PEX6, a gene where loss-of-function variants are known to be pathogenic. 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: Jan 7, 2023

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