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NM_001127649.3(PEX26):c.-3_17delinsTGCAGCCCCCCTCAGGGGGCTCGGGG (p.Met1_Ser6delinsSerProProGlnGlyAlaArgGly) AND multiple conditions

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jun 7, 2021
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:
RCV003798677.3

Allele description [Variation Report for NM_001127649.3(PEX26):c.-3_17delinsTGCAGCCCCCCTCAGGGGGCTCGGGG (p.Met1_Ser6delinsSerProProGlnGlyAlaArgGly)]

NM_001127649.3(PEX26):c.-3_17delinsTGCAGCCCCCCTCAGGGGGCTCGGGG (p.Met1_Ser6delinsSerProProGlnGlyAlaArgGly)

Genes:
LOC130066940:ATAC-STARR-seq lymphoblastoid silent region 13448 [Gene]
PEX26:peroxisomal biogenesis factor 26 [Gene - OMIM - HGNC]
Variant type:
Indel
Cytogenetic location:
22q11.21
Genomic location:
Preferred name:
NM_001127649.3(PEX26):c.-3_17delinsTGCAGCCCCCCTCAGGGGGCTCGGGG (p.Met1_Ser6delinsSerProProGlnGlyAlaArgGly)
HGVS:
  • NC_000022.11:g.18078374_18078393delinsTGCAGCCCCCCTCAGGGGGCTCGGGG
  • NG_008339.1:g.5455_5474delinsTGCAGCCCCCCTCAGGGGGCTCGGGG
  • NG_008339.2:g.5386_5405delinsTGCAGCCCCCCTCAGGGGGCTCGGGG
  • NG_201354.1:g.421_430delinsTGCAGCCCCCCTCAGGGGGCTCGGGG
  • NG_201355.1:g.121_140delinsTGCAGCCCCCCTCAGGGGGCTCGGGG
  • NM_001127649.3:c.-3_17delinsTGCAGCCCCCCTCAGGGGGCTCGGGGMANE SELECT
  • NM_001199319.2:c.-3_17delinsTGCAGCCCCCCTCAGGGGGCTCGGGG
  • NM_017929.6:c.-3_17delinsTGCAGCCCCCCTCAGGGGGCTCGGGG
  • NP_001121121.1:p.Met1_Ser6delinsSerProProGlnGlyAlaArgGly
  • NP_001186248.1:p.Met1_Ser6delinsSerProProGlnGlyAlaArgGly
  • NP_060399.1:p.Met1_Ser6delinsSerProProGlnGlyAlaArgGly
  • NC_000022.10:g.18561140_18561159delinsTGCAGCCCCCCTCAGGGGGCTCGGGG
Molecular consequence:
  • NM_001127649.3:c.-3_17delinsTGCAGCCCCCCTCAGGGGGCTCGGGG - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_001199319.2:c.-3_17delinsTGCAGCCCCCCTCAGGGGGCTCGGGG - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_017929.6:c.-3_17delinsTGCAGCCCCCCTCAGGGGGCTCGGGG - initiator_codon_variant - [Sequence Ontology: SO:0001582]

Condition(s)

Name:
Peroxisome biogenesis disorder 7A (Zellweger)
Synonyms:
Peroxisome biogenesis disorder 7A
Identifiers:
MONDO: MONDO:0013938; MedGen: C3888385; Orphanet: 912; OMIM: 614872
Name:
Peroxisome biogenesis disorder 7B (PBD7B)
Identifiers:
MONDO: MONDO:0013939; MedGen: C3553951; Orphanet: 44; OMIM: 614873

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004582425Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Likely pathogenic
(Jun 7, 2021) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Mutations in novel peroxin gene PEX26 that cause peroxisome-biogenesis disorders of complementation group 8 provide a genotype-phenotype correlation.

Matsumoto N, Tamura S, Furuki S, Miyata N, Moser A, Shimozawa N, Moser HW, Suzuki Y, Kondo N, Fujiki Y.

Am J Hum Genet. 2003 Aug;73(2):233-46. Epub 2003 Jul 8.

PubMed [citation]
PMID:
12851857
PMCID:
PMC1180364

Next-generation sequencing reveals the mutational landscape of clinically diagnosed Usher syndrome: copy number variations, phenocopies, a predominant target for translational read-through, and PEX26 mutated in Heimler syndrome.

Neuhaus C, Eisenberger T, Decker C, Nagl S, Blank C, Pfister M, Kennerknecht I, Müller-Hofstede C, Charbel Issa P, Heller R, Beck B, Rüther K, Mitter D, Rohrschneider K, Steinhauer U, Korbmacher HM, Huhle D, Elsayed SM, Taha HM, Baig SM, Stöhr H, Preising M, et al.

Mol Genet Genomic Med. 2017 Sep;5(5):531-552. doi: 10.1002/mgg3.312.

PubMed [citation]
PMID:
28944237
PMCID:
PMC5606877
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004582425.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. This variant disrupts the initiator methionine in PEX26. If translation initiates from the next in-frame methionine, the PEX26 protein would no longer include the region containing the p.Gly89 amino acid residue. Other variant(s) that disrupt this residue have been observed in individuals with PEX26-related conditions (PMID: 12851857), which suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Disruption of the initiator codon ‚Äãhas been observed in individual(s) with clinical features of Zellweger spectrum disorder (PMID: 12851857, 28944237). This variant is not present in population databases (ExAC no frequency). This sequence change affects the initiator methionine of the PEX26 mRNA. The next in-frame methionine is located at codon 96.

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

Last Updated: Sep 29, 2024