NM_000466.3(PEX1):c.484C>A (p.Pro162Thr) AND Peroxisome biogenesis disorder 1A (Zellweger)

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Feb 10, 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:: RCV003223550.1

Allele description [Variation Report for NM_000466.3(PEX1):c.484C>A (p.Pro162Thr)]

NM_000466.3(PEX1):c.484C>A (p.Pro162Thr)

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.484C>A (p.Pro162Thr)

HGVS:

NC_000007.14:g.92518031G>T
NG_008341.2:g.15501C>A
NM_000466.3:c.484C>AMANE SELECT
NM_001282677.2:c.484C>A
NM_001282678.2:c.-141C>A
NP_000457.1:p.Pro162Thr
NP_001269606.1:p.Pro162Thr
NC_000007.13:g.92147345G>T
NM_000466.2:c.484C>A

Protein change:

P162T

Molecular consequence:

NM_001282678.2:c.-141C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000466.3:c.484C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001282677.2:c.484C>A - missense variant - [Sequence Ontology: SO:0001583]

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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Oxysterol binding protein-like 10 [Mus musculus]
Oxysterol binding protein-like 10 [Mus musculus]
gi|20071006|gb|AAH27256.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003918857	Wangler Lab, Baylor College of Medicine	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Feb 10, 2023)	unknown	research	PubMed (2) [See all records that cite these PMIDs] 29419819, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003918857

Wangler Lab, Baylor College of Medicine

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Feb 10, 2023)

unknown

research

PubMed (2)
[See all records that cite these PMIDs]

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	research

Citations

PubMed

A metabolomic map of Zellweger spectrum disorders reveals novel disease biomarkers.

Wangler MF, Hubert L, Donti TR, Ventura MJ, Miller MJ, Braverman N, Gawron K, Bose M, Moser AB, Jones RO, Rizzo WB, Sutton VR, Sun Q, Kennedy AD, Elsea SH.

Genet Med. 2018 Oct;20(10):1274-1283. doi: 10.1038/gim.2017.262. Epub 2018 Feb 8.

PubMed [citation]

PMID:: 29419819
PMCID:: PMC7605708

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Wangler Lab, Baylor College of Medicine, SCV003918857.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1		not provided	not provided	not provided	research	PubMed (2)

Description

This missense change (c.484C>A) in PEX1 was seen in trans with c.2528G>A (p.G843D) (PM3), a well known pathogenic change to PEX1. This variant is reported in an affected patient by Wangler et al. (PMID: 29419819). The c.484C>A change is predicted to be pathogenic by multiple computational models (PP3), and it is not seen in population databases of healthy individuals (PM2). We interpret this variant to be likely pathogenic.

#	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: Apr 30, 2023

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