NM_001127649.3(PEX26):c.230+1G>T AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 20, 2023
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:: RCV001851574.4

Allele description [Variation Report for NM_001127649.3(PEX26):c.230+1G>T]

NM_001127649.3(PEX26):c.230+1G>T

Gene:

PEX26:peroxisomal biogenesis factor 26 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

22q11.21

Genomic location:

Preferred name:

NM_001127649.3(PEX26):c.230+1G>T

HGVS:

NC_000022.11:g.18078607G>T
NG_008339.1:g.5688G>T
NG_008339.2:g.5619G>T
NM_001127649.3:c.230+1G>TMANE SELECT
NM_001199319.2:c.230+1G>T
NM_017929.6:c.230+1G>T
NC_000022.10:g.18561373G>T
NM_017929.5:c.230+1G>T

Nucleotide change:

IVS2DS, G-T, +1

Links:

OMIM: 608666.0008; dbSNP: rs267608190

NCBI 1000 Genomes Browser:

rs267608190

Molecular consequence:

NM_001127649.3:c.230+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001199319.2:c.230+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
NM_017929.6:c.230+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:: Peroxisome biogenesis disorder 7A (Zellweger)
Synonyms:: Peroxisome biogenesis disorder 7A
Identifiers:: MONDO: MONDO:0013938; MedGen: C3888385; Orphanet: 912; OMIM: 614872

Name:: Peroxisome biogenesis disorder 7B (PBD7B)
Identifiers:: MONDO: MONDO:0013939; MedGen: C3553951; Orphanet: 44; OMIM: 614873

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002228660	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Nov 20, 2023)	germline	clinical testing	PubMed (7) [See all records that cite these PMIDs] 16199547, 12851857, 21031596, 16257970, 27392320, 29947050, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002228660

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Nov 20, 2023)

germline

clinical testing

PubMed (7)
[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

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]

PMID:: 16199547
PMCID:: PMC1735933

Mutations in novel peroxin gene PEX26 that cause peroxisome-biogenesis disorders of complementation group 8 provide a genotype-phenotype correlation.

Matsumoto N, Tamura S, Furuki S, Miyata N, Moser A, Shimozawa N, Moser HW, Suzuki Y, Kondo N, Fujiki Y.

Am J Hum Genet. 2003 Aug;73(2):233-46. Epub 2003 Jul 8.

PubMed [citation]

PMID:: 12851857
PMCID:: PMC1180364

See all PubMed Citations (7)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002228660.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (7)

Description

This sequence change affects a donor splice site in intron 2 of the PEX26 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in PEX26 are known to be pathogenic (PMID: 12851857, 21031596). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individuals with Zellweger syndrome (PMID: 16257970, 27392320, 29947050). This variant is also known as intG231T. ClinVar contains an entry for this variant (Variation ID: 2159). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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

ClinVar

Relating variation to medicine