NM_004813.4(PEX16):c.204G>T (p.Glu68Asp) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 29, 2017
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:: RCV000766831.3

Allele description [Variation Report for NM_004813.4(PEX16):c.204G>T (p.Glu68Asp)]

NM_004813.4(PEX16):c.204G>T (p.Glu68Asp)

Gene:

PEX16:peroxisomal biogenesis factor 16 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11p11.2

Genomic location:

Preferred name:

NM_004813.4(PEX16):c.204G>T (p.Glu68Asp)

HGVS:

NC_000011.10:g.45916248C>A
NG_008460.1:g.6876G>T
NM_004813.4:c.204G>TMANE SELECT
NM_057174.3:c.204G>T
NP_004804.2:p.Glu68Asp
NP_476515.2:p.Glu68Asp
NC_000011.9:g.45937799C>A
NM_004813.2:c.204G>T

Protein change:

E68D

Links:

dbSNP: rs149348130

NCBI 1000 Genomes Browser:

rs149348130

Molecular consequence:

NM_004813.4:c.204G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_057174.3:c.204G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000618593	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Uncertain significance (Jun 29, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000618593

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Uncertain significance
(Jun 29, 2017)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000618593.2

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

Description

The E68D variant in the PEX16 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The E68D variant is observed in 68/10,406 (0.65%) alleles from individuals of African background in the ExAC dataset (Lek et al., 2016). This substitution occurs at a position that is conserved in mammals. However, the E68D variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. We interpret E68D as a variant of uncertain significance.

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

Last Updated: Oct 13, 2024

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