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NM_000286.3(PEX12):c.268_271del (p.Lys90fs)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: Sep 2, 2021)
Last evaluated:
Dec 19, 2020
Accession:
VCV000501646.7
Variation ID:
501646
Description:
4bp deletion
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NM_000286.3(PEX12):c.268_271del (p.Lys90fs)

Allele ID
493070
Variant type
Deletion
Variant length
4 bp
Cytogenetic location
17q12
Genomic location
17: 35577447-35577450 (GRCh38) GRCh38 UCSC
17: 33904466-33904469 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000017.10:g.33904467_33904470del
NC_000017.11:g.35577448_35577451del
NG_008447.1:g.6188_6191del
... more HGVS
Protein change
K90fs
Other names
-
Canonical SPDI
NC_000017.11:35577446:TCTTT:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA8504933
dbSNP: rs61752100
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 2 criteria provided, multiple submitters, no conflicts Aug 7, 2019 RCV000595990.3
Likely pathogenic 1 criteria provided, single submitter Jan 26, 2017 RCV000665252.1
Pathogenic 1 criteria provided, single submitter Aug 2, 2020 RCV000690109.3
Pathogenic 1 criteria provided, single submitter Dec 19, 2020 RCV000781708.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PEX12 - - GRCh38
GRCh37
237 245

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Jan 26, 2017)
criteria provided, single submitter
Method: clinical testing
Peroxisome biogenesis disorder type 3B
Peroxisome biogenesis disorder 3A
Allele origin: unknown
Counsyl
Accession: SCV000789341.1
Submitted: (Jul 10, 2018)
Evidence details
Publications
PubMed (2)
Pathogenic
(Apr 21, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000708096.2
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Pathogenic
(Dec 19, 2020)
criteria provided, single submitter
Method: clinical testing
Peroxisome biogenesis disorders, Zellweger syndrome spectrum
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000919971.2
Submitted: (Dec 31, 2020)
Evidence details
Publications
PubMed (4)
Comment:
Variant summary: PEX12 c.268_271delAAGA (p.Lys90GlufsX3) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein … (more)
Pathogenic
(Aug 02, 2020)
criteria provided, single submitter
Method: clinical testing
Peroxisome biogenesis disorder 3A
Allele origin: germline
Invitae
Accession: SCV000817787.3
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (5)
Comment:
This sequence change creates a premature translational stop signal (p.Lys90Glufs*3) in the PEX12 gene. It is expected to result in an absent or disrupted protein … (more)
Pathogenic
(Aug 07, 2019)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001824666.1
Submitted: (Sep 02, 2021)
Evidence details
Comment:
Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; This … (more)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
Genetic classification and mutational spectrum of more than 600 patients with a Zellweger syndrome spectrum disorder. Ebberink MS Human mutation 2011 PMID: 21031596
The PEX Gene Screen: molecular diagnosis of peroxisome biogenesis disorders in the Zellweger syndrome spectrum. Steinberg S Molecular genetics and metabolism 2004 PMID: 15542397
Genotype-phenotype correlations in disorders of peroxisome biogenesis. Moser HW Molecular genetics and metabolism 1999 PMID: 10527683
Phenotype-genotype relationships in complementation group 3 of the peroxisome-biogenesis disorders. Chang CC American journal of human genetics 1998 PMID: 9792857
PEX12, the pathogenic gene of group III Zellweger syndrome: cDNA cloning by functional complementation on a CHO cell mutant, patient analysis, and characterization of PEX12p. Okumoto K Molecular and cellular biology 1998 PMID: 9632816
Isolation of the human PEX12 gene, mutated in group 3 of the peroxisome biogenesis disorders. Chang CC Nature genetics 1997 PMID: 9090384
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=PEX12 - - - -

Text-mined citations for rs61752100...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021