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NM_002617.4(PEX10):c.416C>T (p.Ser139Leu) AND Peroxisome biogenesis disorder, complementation group 7

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 26, 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:
RCV002928758.3

Allele description [Variation Report for NM_002617.4(PEX10):c.416C>T (p.Ser139Leu)]

NM_002617.4(PEX10):c.416C>T (p.Ser139Leu)

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.416C>T (p.Ser139Leu)
HGVS:
  • NC_000001.11:g.2408636G>A
  • NG_008342.1:g.8936C>T
  • NG_088790.1:g.55G>A
  • NM_001374425.1:c.416C>T
  • NM_001374426.1:c.-17C>T
  • NM_001374427.1:c.-17C>T
  • NM_002617.4:c.416C>TMANE SELECT
  • NM_153818.2:c.416C>T
  • NP_001361354.1:p.Ser139Leu
  • NP_002608.1:p.Ser139Leu
  • NP_722540.1:p.Ser139Leu
  • NC_000001.10:g.2340075G>A
  • NR_164636.1:n.535C>T
Protein change:
S139L
Molecular consequence:
  • NM_001374426.1:c.-17C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001374427.1:c.-17C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001374425.1:c.416C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_002617.4:c.416C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_153818.2:c.416C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_164636.1:n.535C>T - 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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003275143Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jan 26, 2022) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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, SCV003275143.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

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. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. This variant has not been reported in the literature in individuals affected with PEX10-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces serine, which is neutral and polar, with leucine, which is neutral and non-polar, at codon 139 of the PEX10 protein (p.Ser139Leu).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024