NM_000466.3(PEX1):c.496del (p.Tyr166fs) AND multiple conditions

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Mar 5, 2022
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:: RCV002308097.2

Allele description [Variation Report for NM_000466.3(PEX1):c.496del (p.Tyr166fs)]

NM_000466.3(PEX1):c.496del (p.Tyr166fs)

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.496del (p.Tyr166fs)

HGVS:

NC_000007.14:g.92518020del
NG_008341.2:g.15513del
NM_000466.3:c.496delMANE SELECT
NM_001282677.2:c.496del
NM_001282678.2:c.-129del
NP_000457.1:p.Tyr166fs
NP_001269606.1:p.Tyr166fs
NC_000007.13:g.92147334del

Protein change:

Y166fs

Molecular consequence:

NM_001282678.2:c.-129del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000466.3:c.496del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001282677.2:c.496del - frameshift variant - [Sequence Ontology: SO:0001589]

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002601786	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2021))	Likely pathogenic (Mar 5, 2022)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002601786

Myriad Genetics, Inc.

criteria provided, single submitter

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

Likely pathogenic
(Mar 5, 2022)

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., SCV002601786.2

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

Description

NM_000466.2(PEX1):c.496delT(Y166Mfs*44) is expected to be pathogenic in the context of peroxisome biogenesis disorder type 1. This variant is predicted to lead to an abnormal or absent protein product due to the creation of a premature termination codon in PEX1, 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: Dec 24, 2022

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