22-18078374-GTTATGAAGAGCGATTCTTC-TGCAGCCCCCCTCAGGGGGCTCGGGG

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The NM_001127649.3(PEX26):c.-3_17delinsTGCAGCCCCCCTCAGGGGGCTCGGGG variant causes a start lost, 5 prime UTR change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: PEX26 NM_001127649.3 start_lost, 5_prime_UTR
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 4.42

Genes affected

PEX26 (HGNC:22965): (peroxisomal biogenesis factor 26) This gene belongs to the peroxin-26 gene family. It is probably required for protein import into peroxisomes. It anchors PEX1 and PEX6 to peroxisome membranes, possibly to form heteromeric AAA ATPase complexes required for the import of proteins into peroxisomes. Defects in this gene are the cause of peroxisome biogenesis disorder complementation group 8 (PBD-CG8). PBD refers to a group of peroxisomal disorders arising from a failure of protein import into the peroxisomal membrane or matrix. The PBD group is comprised of four disorders: Zellweger syndrome (ZWS), neonatal adrenoleukodystrophy (NALD), infantile Refsum disease (IRD), and classical rhizomelic chondrodysplasia punctata (RCDP). Alternatively spliced transcript variants have been identified for this gene. [provided by RefSeq, Dec 2010]

(HGNC:):

ACMG classification

Verdict is Pathogenic. Variant got 12 ACMG points.

• PVS1: Start lost variant, no new inframe start found.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 22-18078374-GTTATGAAGAGCGATTCTTC-TGCAGCCCCCCTCAGGGGGCTCGGGG is Pathogenic according to our data. Variant chr22-18078374-GTTATGAAGAGCGATTCTTC-TGCAGCCCCCCTCAGGGGGCTCGGGG is described in ClinVar as [Likely_pathogenic]. Clinvar id is 2934975.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PEX26	NM_001127649.3	c.-3_17delinsTGCAGCCCCCCTCAGGGGGCTCGGGG		start_lost, 5_prime_UTR_variant	1/5	ENST00000399744.8
PEX26	NM_001199319.2	c.-3_17delinsTGCAGCCCCCCTCAGGGGGCTCGGGG		start_lost, 5_prime_UTR_variant	2/5
PEX26	NM_017929.6	c.-3_17delinsTGCAGCCCCCCTCAGGGGGCTCGGGG		start_lost, 5_prime_UTR_variant	2/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PEX26	ENST00000399744.8	c.-3_17delinsTGCAGCCCCCCTCAGGGGGCTCGGGG		start_lost, 5_prime_UTR_variant	1/5	1	NM_001127649.3	P1
	ENST00000607927.1	n.492_511delinsCCCCGAGCCCCCTGAGGGGGGCTGCA		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Peroxisome biogenesis disorder 7B;C3888385:Peroxisome biogenesis disorder 7A (Zellweger) Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Invitae

Jun 07, 2021

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. -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr22-18561140;