NM_002618.4(PEX13):c.86C>G (p.Thr29Ser) AND Peroxisome biogenesis disorder 11A (Zellweger)

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 13, 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:: RCV001344157.5

Allele description

NM_002618.4(PEX13):c.86C>G (p.Thr29Ser)

Genes:

PEX13:peroxisomal biogenesis factor 13 [Gene - OMIM - HGNC]
PUS10:pseudouridine synthase 10 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2p15

Genomic location:

Preferred name:

NM_002618.4(PEX13):c.86C>G (p.Thr29Ser)

HGVS:

NC_000002.12:g.61017845C>G
NG_008665.1:g.5169C>G
NM_001322127.1:c.-623+163G>C
NM_002618.4:c.86C>GMANE SELECT
NM_144709.4:c.-16+163G>CMANE SELECT
NP_002609.1:p.Thr29Ser
NC_000002.11:g.61244980C>G

Protein change:

T29S

Links:

dbSNP: rs543856265

NCBI 1000 Genomes Browser:

rs543856265

Molecular consequence:

NM_001322127.1:c.-623+163G>C - intron variant - [Sequence Ontology: SO:0001627]
NM_144709.4:c.-16+163G>C - intron variant - [Sequence Ontology: SO:0001627]
NM_002618.4:c.86C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Peroxisome biogenesis disorder 11A (Zellweger)
Synonyms:: Peroxisome biogenesis disorder 11A
Identifiers:: MONDO: MONDO:0013949; MedGen: C3554000; Orphanet: 912; OMIM: 614883

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001538193	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 13, 2022)	germline	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

SCV001538193

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 13, 2022)

germline

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

Citations

PubMed

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 Invitae, SCV001538193.3

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

Description

This sequence change replaces threonine, which is neutral and polar, with serine, which is neutral and polar, at codon 29 of the PEX13 protein (p.Thr29Ser). This variant is present in population databases (rs543856265, gnomAD 0.04%). This variant has not been reported in the literature in individuals affected with PEX13-related conditions. ClinVar contains an entry for this variant (Variation ID: 1040499). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The serine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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 1, 2024

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