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NM_000286.3(PEX12):c.126+1G>C AND Peroxisome biogenesis disorder 3A (Zellweger)

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 9, 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:
RCV003828630.1

Allele description [Variation Report for NM_000286.3(PEX12):c.126+1G>C]

NM_000286.3(PEX12):c.126+1G>C

Gene:
PEX12:peroxisomal biogenesis factor 12 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17q12
Genomic location:
Preferred name:
NM_000286.3(PEX12):c.126+1G>C
HGVS:
  • NC_000017.11:g.35577895C>G
  • NG_008447.1:g.5743G>C
  • NG_136277.1:g.161C>G
  • NM_000286.3:c.126+1G>CMANE SELECT
  • NC_000017.10:g.33904914C>G
Molecular consequence:
  • NM_000286.3:c.126+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
Peroxisome biogenesis disorder 3A (Zellweger)
Synonyms:
PEROXISOMAL BIOGENESIS DISORDER 3A (ZELLWEGER); Peroxisome biogenesis disorder 3A
Identifiers:
MONDO: MONDO:0013927; MedGen: C3553929; Orphanet: 912; OMIM: 614859

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004621832Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Oct 9, 2023) 		germlineclinical testing

PubMed (6)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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

Isolation of the human PEX12 gene, mutated in group 3 of the peroxisome biogenesis disorders.

Chang CC, Lee WH, Moser H, Valle D, Gould SJ.

Nat Genet. 1997 Apr;15(4):385-8.

PubMed [citation]
PMID:
9090384
See all PubMed Citations (6)

Details of each submission

From Invitae, SCV004621832.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (6)

Description

This sequence change affects a donor splice site in intron 1 of the PEX12 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 PEX12 are known to be pathogenic (PMID: 9090384, 9632816, 21031596). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individuals with PEX12-related conditions (PMID: 9792857, 21031596). 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.

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

Last Updated: Mar 5, 2024