NM_001127649.3(PEX26):c.153C>A (p.Phe51Leu) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 4, 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:: RCV001861193.5

Allele description [Variation Report for NM_001127649.3(PEX26):c.153C>A (p.Phe51Leu)]

NM_001127649.3(PEX26):c.153C>A (p.Phe51Leu)

Gene:

PEX26:peroxisomal biogenesis factor 26 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

22q11.21

Genomic location:

Preferred name:

NM_001127649.3(PEX26):c.153C>A (p.Phe51Leu)

HGVS:

NC_000022.11:g.18078529C>A
NG_008339.1:g.5610C>A
NM_001127649.3:c.153C>AMANE SELECT
NM_001199319.2:c.153C>A
NM_017929.6:c.153C>A
NP_001121121.1:p.Phe51Leu
NP_001186248.1:p.Phe51Leu
NP_060399.1:p.Phe51Leu
NC_000022.10:g.18561295C>A
NM_017929.5:c.153C>A

Protein change:

F51L

Links:

dbSNP: rs777633990

NCBI 1000 Genomes Browser:

rs777633990

Molecular consequence:

NM_001127649.3:c.153C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001199319.2:c.153C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_017929.6:c.153C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Peroxisome biogenesis disorder 7A (Zellweger)
Synonyms:: Peroxisome biogenesis disorder 7A
Identifiers:: MONDO: MONDO:0013938; MedGen: C3888385; Orphanet: 912; OMIM: 614872

Name:: Peroxisome biogenesis disorder 7B (PBD7B)
Identifiers:: MONDO: MONDO:0013939; MedGen: C3553951; Orphanet: 44; OMIM: 614873

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gi|126582420|gnl|dbEST|45096915|gb| 556.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002222666	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Feb 4, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 30446579, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002222666

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Feb 4, 2022)

germline

clinical testing

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	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A newly identified mutation in the PEX26 gene is associated with a milder form of Zellweger spectrum disorder.

Tanaka AJ, Okumoto K, Tamura S, Abe Y, Hirsch Y, Deng L, Ekstein J, Chung WK, Fujiki Y.

Cold Spring Harb Mol Case Stud. 2019 Feb 1;5(1). doi:pii: a003483. 10.1101/mcs.a003483. Print 2019 Feb.

PubMed [citation]

PMID:: 30446579
PMCID:: PMC6371744

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002222666.2

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

Description

This sequence change replaces phenylalanine, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 51 of the PEX26 protein (p.Phe51Leu). This variant is present in population databases (rs777633990, gnomAD 0.05%). This variant has not been reported in the literature in individuals affected with PEX26-related conditions. ClinVar contains an entry for this variant (Variation ID: 340750). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C15"). Experimental studies have shown that this missense change affects PEX26 function (PMID: 30446579). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Sep 29, 2024

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