NM_000286.3(PEX12):c.961_964del (p.Gly321fs) AND Peroxisome biogenesis disorder 3A

Clinical significance:Pathogenic (Last evaluated: Aug 11, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001382391.1

Allele description [Variation Report for NM_000286.3(PEX12):c.961_964del (p.Gly321fs)]

NM_000286.3(PEX12):c.961_964del (p.Gly321fs)

Gene:
PEX12:peroxisomal biogenesis factor 12 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
17q12
Genomic location:
Preferred name:
NM_000286.3(PEX12):c.961_964del (p.Gly321fs)
HGVS:
  • NC_000017.11:g.35575900_35575903del
  • NG_008447.1:g.7737_7740del
  • NM_000286.3:c.961_964delMANE SELECT
  • NP_000277.1:p.Gly321fs
  • NC_000017.10:g.33902917_33902920delAGCC
  • NC_000017.10:g.33902919_33902922del
  • NM_000286.2:c.961_964delGGCT
Protein change:
G321fs
Links:
dbSNP: rs749650201
NCBI 1000 Genomes Browser:
rs749650201
Molecular consequence:
  • NM_000286.3:c.961_964del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Peroxisome biogenesis disorder 3A (PBD3A)
Synonyms:
PEROXISOMAL BIOGENESIS DISORDER 3A (ZELLWEGER)
Identifiers:
MONDO: MONDO:0013927; MedGen: C3553929; Orphanet: 912; OMIM: 614859

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001581142Invitaecriteria provided, single submitter
Pathogenic
(Aug 11, 2020)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV001581142.1

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

Description

This sequence change results in a premature translational stop signal in the PEX12 gene (p.Gly321Metfs*12). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 39 amino acids of the PEX12 protein. This variant is present in population databases (rs749650201, ExAC 0.02%). This variant has not been reported in the literature in individuals with PEX12-related conditions. ClinVar contains an entry for this variant (Variation ID: 558619). This variant disrupts the C-terminus of the PEX12 protein. Other variant(s) that disrupt this region (p.Gln337*) have been determined to be pathogenic (Invitae). This suggests that variants that disrupt this region of the protein are likely to be causative of disease. 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: Jan 8, 2022

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