rs1554128347

Variant names:

• chr6-42978266-TACCTGAATTCTGAGCTCTCCCATTTCCAGGGGGTCACAGCCAAGATTAAAAGCCAAAGTGGCAGGGACAAGCGCCAGTCCGTCAGCGAGGGGCTCTCCCAGCGGTCCAGAGCCGGGTCCCAGTCTATCAGAGAGGTCCCAGCGAGGTTCTAGGACCTGCACCCTAGCCAAGTGCGGCTGTGAAGTGTTCGATGACTCTCTGGCCTGGGCCACCCACACCCATTCGCCCTGGAAGAGGCCAAGGCCACGGAGACAGCTCCGGCTC-T
• rs1554128347
• NM_000287.4:c.621_882+2del

Variant summary

Our verdict is Likely pathogenic. The variant received 9 ACMG points: 9P and 0B. PVS1 PP5

The NM_000287.4(PEX6):​c.621_882+2del​(p.Ser208fs) variant causes a frameshift, splice donor, splice region, intron change. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. V207V) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 31)
• Consequence: PEX6 NM_000287.4 frameshift, splice_donor, splice_region, intron
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 4.55
• Publications: 0 publications found

Genes affected

PEX6 (HGNC:8859): (peroxisomal biogenesis factor 6) This gene encodes a member of the AAA (ATPases associated with diverse cellular activities) family of ATPases. This member is a predominantly cytoplasmic protein, which plays a direct role in peroxisomal protein import and is required for PTS1 (peroxisomal targeting signal 1, a C-terminal tripeptide of the sequence ser-lys-leu) receptor activity. Mutations in this gene cause peroxisome biogenesis disorders of complementation group 4 and complementation group 6. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]

PEX6 Gene-Disease associations (from GenCC):

• peroxisome biogenesis disorder

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• peroxisome biogenesis disorder 4A (Zellweger)

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P, Myriad Women’s Health
• peroxisome biogenesis disorder 4B

  Inheritance: AR Classification: DEFINITIVE Submitted by: G2P
• Heimler syndrome 2

  Inheritance: AR Classification: MODERATE Submitted by: G2P
• autosomal recessive cerebellar ataxia-blindness-deafness syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• Zellweger spectrum disorders

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Likely_pathogenic. The variant received 9 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PP5: Variant 6-42978266-TACCTGAATTCTGAGCTCTCCCATTTCCAGGGGGTCACAGCCAAGATTAAAAGCCAAAGTGGCAGGGACAAGCGCCAGTCCGTCAGCGAGGGGCTCTCCCAGCGGTCCAGAGCCGGGTCCCAGTCTATCAGAGAGGTCCCAGCGAGGTTCTAGGACCTGCACCCTAGCCAAGTGCGGCTGTGAAGTGTTCGATGACTCTCTGGCCTGGGCCACCCACACCCATTCGCCCTGGAAGAGGCCAAGGCCACGGAGACAGCTCCGGCTC-T is Pathogenic according to our data. Variant chr6-42978266-TACCTGAATTCTGAGCTCTCCCATTTCCAGGGGGTCACAGCCAAGATTAAAAGCCAAAGTGGCAGGGACAAGCGCCAGTCCGTCAGCGAGGGGCTCTCCCAGCGGTCCAGAGCCGGGTCCCAGTCTATCAGAGAGGTCCCAGCGAGGTTCTAGGACCTGCACCCTAGCCAAGTGCGGCTGTGAAGTGTTCGATGACTCTCTGGCCTGGGCCACCCACACCCATTCGCCCTGGAAGAGGCCAAGGCCACGGAGACAGCTCCGGCTC-T is described in ClinVar as Pathogenic. ClinVar VariationId is 8125.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PEX6	NM_000287.4	c.621_882+2del	p.Ser208fs	frameshift_variant, splice_donor_variant, splice_region_variant, intron_variant	Exon 1 of 17	ENST00000304611.13	NP_000278.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PEX6	ENST00000304611.13	c.621_882+2del	p.Ser208fs	frameshift_variant, splice_donor_variant, splice_region_variant, intron_variant	Exon 1 of 17	1	NM_000287.4	ENSP00000303511.8
PEX6	ENST00000244546.4	c.621_882+2del	p.Ser208fs	frameshift_variant, splice_donor_variant, splice_region_variant, intron_variant	Exon 1 of 15	1		ENSP00000244546.4

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Peroxisome biogenesis disorder 4B Pathogenic:1

Jan 01, 2001

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		4.5
Mutation Taster		=7/193	disease causing (ClinVar)

Splicing

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

Other links and lift over

dbSNP: rs1554128347; hg19: chr6-42946004;