NM_000287.4(PEX6):c.2082del (p.Gly695fs) AND Peroxisome biogenesis disorder

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 19, 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:: RCV001052376.6

Allele description [Variation Report for NM_000287.4(PEX6):c.2082del (p.Gly695fs)]

NM_000287.4(PEX6):c.2082del (p.Gly695fs)

Gene:

PEX6:peroxisomal biogenesis factor 6 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

6p21.1

Genomic location:

Preferred name:

NM_000287.4(PEX6):c.2082del (p.Gly695fs)

HGVS:

NC_000006.12:g.42966538del
NG_008370.1:g.17707del
NM_000287.4:c.2082delMANE SELECT
NM_001316313.2:c.1818del
NP_000278.3:p.Gly695fs
NP_001303242.1:p.Gly607fs
NC_000006.11:g.42934275del
NC_000006.11:g.42934276del
NM_000287.3:c.2082del
NM_000287.3:c.2082delT
NR_133009.2:n.2113del

Protein change:

G607fs

Links:

dbSNP: rs766483138

NCBI 1000 Genomes Browser:

rs766483138

Molecular consequence:

NM_000287.4:c.2082del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001316313.2:c.1818del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_133009.2:n.2113del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Peroxisome biogenesis disorder (PBD, ZSS)
Synonyms:: PEROXISOME BIOGENESIS DISORDER (NEONATAL ADRENOLEUKODYSTROPHY/INFANTILE REFSUM DISEASE); INFANTILE PHYTANIC ACID STORAGE DISEASE; PEROXISOME BIOGENESIS DISORDER (NALD/IRD); See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0019234; MedGen: C1832200; OMIM: PS214100

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Limbic Lobe
Limbic Lobe
The medial surface of the cerebral hemisphere around the brain stem.<br/>Year introduced: 2015

MeSH
Substantia Innominata
Substantia Innominata
Tissue in the BASAL FOREBRAIN inferior to the anterior perforated substance, and anterior to the GLOBUS PALLIDUS and ansa lenticularis. It contains the BASAL NUCLEUS OF MEYNER...<br/>Year introduced: 1991(1984)

MeSH
Hypothalamus
Hypothalamus
Ventral part of the DIENCEPHALON extending from the region of the OPTIC CHIASM to the caudal border of the MAMMILLARY BODIES and forming the inferior and lateral walls of the ...<br/>

MeSH
Glymphatic System
Glymphatic System
A vascular waste clearance system in the brain analogous to the lymphatic system that facilitates transporting of solutes and waste products from CEREBROSPINAL FLUID (CSF) and...<br/>Year introduced: 2019

MeSH

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001216585	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 19, 2022)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 8670792, 19877282, 21031596, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001216585

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 19, 2022)

germline

clinical testing

PubMed (4)
[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

The peroxisome biogenesis disorder group 4 gene, PXAAA1, encodes a cytoplasmic ATPase required for stability of the PTS1 receptor.

Yahraus T, Braverman N, Dodt G, Kalish JE, Morrell JC, Moser HW, Valle D, Gould SJ.

EMBO J. 1996 Jun 17;15(12):2914-23.

PubMed [citation]

PMID:: 8670792
PMCID:: PMC450231

Spectrum of PEX6 mutations in Zellweger syndrome spectrum patients.

Ebberink MS, Kofster J, Wanders RJ, Waterham HR.

Hum Mutat. 2010 Jan;31(1):E1058-70. doi: 10.1002/humu.21153.

PubMed [citation]

PMID:: 19877282

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001216585.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This sequence change creates a premature translational stop signal (p.Gly695Glufs*19) in the PEX6 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PEX6 are known to be pathogenic (PMID: 8670792, 19877282, 21031596). This variant is present in population databases (rs766483138, gnomAD 0.002%). This variant has not been reported in the literature in individuals affected with PEX6-related conditions. ClinVar contains an entry for this variant (Variation ID: 553235). For these reasons, this variant has been classified as Pathogenic.

#	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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