NM_002617.4(PEX10):c.307C>G (p.Pro103Ala) AND Peroxisome biogenesis disorder, complementation group 7

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 12, 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:: RCV002047103.3

Allele description [Variation Report for NM_002617.4(PEX10):c.307C>G (p.Pro103Ala)]

NM_002617.4(PEX10):c.307C>G (p.Pro103Ala)

Gene:

PEX10:peroxisomal biogenesis factor 10 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p36.32

Genomic location:

Preferred name:

NM_002617.4(PEX10):c.307C>G (p.Pro103Ala)

HGVS:

NC_000001.11:g.2408745G>C
NG_008342.1:g.8827C>G
NM_001374425.1:c.307C>G
NM_001374426.1:c.-126C>G
NM_001374427.1:c.-126C>G
NM_002617.4:c.307C>GMANE SELECT
NM_153818.2:c.307C>G
NP_001361354.1:p.Pro103Ala
NP_002608.1:p.Pro103Ala
NP_722540.1:p.Pro103Ala
NC_000001.10:g.2340184G>C
NR_164636.1:n.426C>G

Protein change:

P103A

Links:

dbSNP: rs1299562078

NCBI 1000 Genomes Browser:

rs1299562078

Molecular consequence:

NM_001374426.1:c.-126C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001374427.1:c.-126C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001374425.1:c.307C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_002617.4:c.307C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_153818.2:c.307C>G - missense variant - [Sequence Ontology: SO:0001583]
NR_164636.1:n.426C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Peroxisome biogenesis disorder, complementation group 7 (CG7)
Synonyms:: Peroxisome biogenesis disorder, complementation group B
Identifiers:: MedGen: C1864399

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Protein
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Gene ID:114444

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002111581	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 12, 2021)	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

SCV002111581

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 12, 2021)

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV002111581.2

#	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 proline with alanine at codon 103 of the PEX10 protein (p.Pro103Ala). The proline residue is highly conserved and there is a small physicochemical difference between proline and alanine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with PEX10-related conditions. 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: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). 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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