NM_000288.4(PEX7):c.549G>A (p.Trp183Ter) AND Peroxisome biogenesis disorder 9B

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: Aug 20, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV003476859.3

Allele description [Variation Report for NM_000288.4(PEX7):c.549G>A (p.Trp183Ter)]

NM_000288.4(PEX7):c.549G>A (p.Trp183Ter)

Gene:

PEX7:peroxisomal biogenesis factor 7 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

6q23.3

Genomic location:

Preferred name:

NM_000288.4(PEX7):c.549G>A (p.Trp183Ter)

HGVS:

NC_000006.12:g.136866649G>A
NG_008462.1:g.49070G>A
NM_000288.4:c.549G>AMANE SELECT
NM_001410945.1:c.435G>A
NP_000279.1:p.Trp183Ter
NP_001397874.1:p.Trp145Ter
NC_000006.11:g.137187787G>A

Protein change:

W145*

Molecular consequence:

NM_000288.4:c.549G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001410945.1:c.435G>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Peroxisome biogenesis disorder 9B
Synonyms:: PEROXISOME BIOGENESIS DISORDER, PEX7-RELATED, ATYPICAL; Refsum disease, adult, 2
Identifiers:: MONDO: MONDO:0013945; MedGen: C2749346; Orphanet: 773; OMIM: 614879

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Hyperolius parkeri voucher MVZ:Herp:233913 tyrosinase (TYR) gene, partial cds
Hyperolius parkeri voucher MVZ:Herp:233913 tyrosinase (TYR) gene, partial cds
gi|1685833800|gb|MK498213.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004203901	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Aug 20, 2023)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004396378	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Mar 16, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 12325024, 12522768, 20301447, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004203901

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Aug 20, 2023)

unknown

clinical testing

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

SCV004396378

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Mar 16, 2023)

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Mutation analysis of PEX7 in 60 probands with rhizomelic chondrodysplasia punctata and functional correlations of genotype with phenotype.

Braverman N, Chen L, Lin P, Obie C, Steel G, Douglas P, Chakraborty PK, Clarke JT, Boneh A, Moser A, Moser H, Valle D.

Hum Mutat. 2002 Oct;20(4):284-97.

PubMed [citation]

PMID:: 12325024

See all PubMed Citations (5)

Details of each submission

From Baylor Genetics, SCV004203901.1

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

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004396378.1

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

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with PEX7-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.0009%). This sequence change creates a premature translational stop signal (p.Trp183*) in the PEX7 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PEX7 are known to be pathogenic (PMID: 12325024, 12522768, 20301447).

#	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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