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NM_000286.3(PEX12):c.625C>T (p.Gln209Ter)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
3 (Most recent: Jan 7, 2021)
Last evaluated:
Mar 3, 2020
Accession:
VCV000555548.5
Variation ID:
555548
Description:
single nucleotide variant
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NM_000286.3(PEX12):c.625C>T (p.Gln209Ter)

Allele ID
548348
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
17q12
Genomic location
17: 35577093 (GRCh38) GRCh38 UCSC
17: 33904112 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000017.10:g.33904112G>A
NC_000017.11:g.35577093G>A
NG_008447.1:g.6545C>T
NM_000286.3:c.625C>T MANE Select NP_000277.1:p.Gln209Ter nonsense
Protein change
Q209*
Other names
-
Canonical SPDI
NC_000017.11:35577092:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
dbSNP: rs61752106
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 1 criteria provided, single submitter Dec 12, 2017 RCV000671389.1
Pathogenic 1 criteria provided, single submitter Aug 13, 2018 RCV000781711.1
Pathogenic 1 criteria provided, single submitter Mar 3, 2020 RCV000819199.3
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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
(Dec 12, 2017)
criteria provided, single submitter
Method: clinical testing
Peroxisome biogenesis disorder type 3B
Peroxisome biogenesis disorder 3A
Allele origin: unknown
Counsyl
Accession: SCV000796361.1
Submitted: (Jul 10, 2018)
Evidence details
Publications
PubMed (2)
Pathogenic
(Aug 13, 2018)
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: SCV000919974.1
Submitted: (Apr 24, 2019)
Evidence details
Publications
PubMed (3)
Comment:
Variant summary: PEX12 c.625C>T (p.Gln209X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein … (more)
Pathogenic
(Mar 03, 2020)
criteria provided, single submitter
Method: clinical testing
Peroxisome biogenesis disorder 3A
Allele origin: germline
Invitae
Accession: SCV000959846.3
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (4)
Comment:
This sequence change creates a premature translational stop signal (p.Gln209*) in the PEX12 gene. It is expected to result in an absent or disrupted protein … (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
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
Novel mutations in the PEX2 gene of four unrelated patients with a peroxisome biogenesis disorder. Gootjes J Pediatric research 2004 PMID: 14630978
Novel mutations in the PEX12 gene of patients with a peroxisome biogenesis disorder. Gootjes J European journal of human genetics : EJHG 2004 PMID: 14571262
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

Text-mined citations for rs61752106...

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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