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NM_000287.4(PEX6):c.600del (p.Thr201fs) AND Peroxisome biogenesis disorder 4A (Zellweger)

Germline classification:
Likely pathogenic (1 submission)
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:
RCV003314428.1

Allele description [Variation Report for NM_000287.4(PEX6):c.600del (p.Thr201fs)]

NM_000287.4(PEX6):c.600del (p.Thr201fs)

Gene:
PEX6:peroxisomal biogenesis factor 6 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
6p21.1
Genomic location:
Preferred name:
NM_000287.4(PEX6):c.600del (p.Thr201fs)
HGVS:
  • NC_000006.12:g.42978553del
  • NG_008370.1:g.5693del
  • NG_108258.1:g.213del
  • NM_000287.4:c.600delMANE SELECT
  • NM_001316313.2:c.600del
  • NP_000278.3:p.Thr201fs
  • NP_001303242.1:p.Thr201fs
  • NC_000006.11:g.42946291del
  • NR_133009.2:n.631del
Protein change:
T201fs
Molecular consequence:
  • NM_000287.4:c.600del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001316313.2:c.600del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NR_133009.2:n.631del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Peroxisome biogenesis disorder 4A (Zellweger) (PBD4A)
Synonyms:
Zellweger syndrome spectrum (PEX6-related)
Identifiers:
MONDO: MONDO:0013930; MedGen: C3553936; Orphanet: 912; OMIM: 614862

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV0040137603billion
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenicunknownclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyes1not providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From 3billion, SCV004013760.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

The variant is not observed in the gnomAD v2.1.1 dataset. The variant is predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant. similarly affected family member was shared with this variant (3billion database). Therefore, this variant is classified as Likely pathogenic according to the recommendation of ACMG/AMP guideline.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Jul 22, 2023