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NM_000287.4(PEX6):c.2735C>T (p.Ala912Val) 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:
RCV001823180.3

Allele description [Variation Report for NM_000287.4(PEX6):c.2735C>T (p.Ala912Val)]

NM_000287.4(PEX6):c.2735C>T (p.Ala912Val)

Gene:
PEX6:peroxisomal biogenesis factor 6 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
6p21.1
Genomic location:
Preferred name:
NM_000287.4(PEX6):c.2735C>T (p.Ala912Val)
HGVS:
  • NC_000006.12:g.42964861G>A
  • NG_008370.1:g.19383C>T
  • NG_008396.1:g.9100G>A
  • NM_000287.4:c.2735C>TMANE SELECT
  • NM_001316313.2:c.2471C>T
  • NP_000278.3:p.Ala912Val
  • NP_001303242.1:p.Ala824Val
  • NC_000006.11:g.42932599G>A
  • NM_000287.3:c.2735C>T
  • NM_000287.3:c.[2735C>T]
  • NR_133009.2:n.2519C>T
Protein change:
A824V
Links:
dbSNP: rs62641232
NCBI 1000 Genomes Browser:
rs62641232
Molecular consequence:
  • NM_000287.4:c.2735C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001316313.2:c.2471C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_133009.2:n.2519C>T - 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

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV002073036Neuberg Centre For Genomic Medicine, NCGM
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenicgermlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot 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 Neuberg Centre For Genomic Medicine, NCGM, SCV002073036.1

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

Description

The missense variant p.A912V in PEX6 (NM_000287.4) has been reported previously in individual(s) with Zellweger syndrome (Guissart C et al; Wang X et al ). The variant has been submitted to ClinVar as Likely Pathogenic. The p.A912V variant is observed in 1/1,13,724 (0.0009%) alleles from individuals of European (Non-Finnish) background in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. The p.A912V missense variant is predicted to be damaging by both SIFT and PolyPhen2. The alanine residue at codon 912 of PEX6 is conserved in all mammalian species. The nucleotide c.2735 in PEX6 is predicted conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Likely Pathogenic.

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

Last Updated: Sep 29, 2024