ENST00000541292.6:n.-88T>C

Variant names:

• chr6-136822476-C-.
• NM_000288.4:c.-190C>.

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The ENST00000541292.6(PEX7):​n.-190C>. variant causes a upstream gene change. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 N/A (N/A hom., cov:)
  • Exomes 𝑓: N/A (N/A hom.)
• Consequence: PEX7 ENST00000541292.6 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

Genes affected

PEX7 (HGNC:8860): (peroxisomal biogenesis factor 7) This gene encodes the cytosolic receptor for the set of peroxisomal matrix enzymes targeted to the organelle by the peroxisome targeting signal 2 (PTS2). Defects in this gene cause peroxisome biogenesis disorders (PBDs), which are characterized by multiple defects in peroxisome function. There are at least 14 complementation groups for PBDs, with more than one phenotype being observed in cases falling into particular complementation groups. Although the clinical features of PBD patients vary, cells from all PBD patients exhibit a defect in the import of one or more classes of peroxisomal matrix proteins into the organelle. Defects in this gene have been associated with PBD complementation group 11 (PBD-CG11) disorders, rhizomelic chondrodysplasia punctata type 1 (RCDP1), and Refsum disease (RD). [provided by RefSeq, Oct 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PEX7	NM_000288.4	c.-190C>.		upstream_gene_variant		ENST00000318471.5	NP_000279.1
PEX7	XM_006715502.3	c.-190C>.		upstream_gene_variant			XP_006715565.1
PEX7	XM_047418874.1	c.-190C>.		upstream_gene_variant			XP_047274830.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PEX7	ENST00000318471.5	c.-190C>.		upstream_gene_variant		1	NM_000288.4	ENSP00000315680.3
PEX7	ENST00000367756.8	c.-190C>.		upstream_gene_variant		3		ENSP00000356730.4
PEX7	ENST00000541292.6	n.-190C>.		upstream_gene_variant		5		ENSP00000441004.1
PEX7	ENST00000678593.1	n.-190C>.		upstream_gene_variant				ENSP00000503841.1

Frequencies

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

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

ClinVar

Not reported in ClinVar

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: chr6-137143614;