rs267608252
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000288.4(PEX7):c.-45C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000017 in 1,353,968 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).
Frequency
Genomes: not found (cov: 35)
Exomes 𝑓: 0.000017 ( 0 hom. )
Consequence
PEX7
NM_000288.4 5_prime_UTR
NM_000288.4 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.09
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.73).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PEX7 | NM_000288.4 | c.-45C>T | 5_prime_UTR_variant | 1/10 | ENST00000318471.5 | ||
PEX7 | XM_006715502.3 | c.-45C>T | 5_prime_UTR_variant | 1/7 | |||
PEX7 | XM_047418874.1 | c.-45C>T | 5_prime_UTR_variant | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PEX7 | ENST00000318471.5 | c.-45C>T | 5_prime_UTR_variant | 1/10 | 1 | NM_000288.4 | P1 | ||
PEX7 | ENST00000367756.8 | c.-45C>T | 5_prime_UTR_variant | 1/4 | 3 | ||||
PEX7 | ENST00000541292.6 | c.-45C>T | 5_prime_UTR_variant, NMD_transcript_variant | 1/11 | 5 | ||||
PEX7 | ENST00000678593.1 | upstream_gene_variant |
Frequencies
GnomAD3 genomes ? Cov.: 35
GnomAD3 genomes
?
Cov.:
35
GnomAD4 exome AF: 0.0000170 AC: 23AN: 1353968Hom.: 0 Cov.: 28 AF XY: 0.0000149 AC XY: 10AN XY: 669388
GnomAD4 exome
AF:
AC:
23
AN:
1353968
Hom.:
Cov.:
28
AF XY:
AC XY:
10
AN XY:
669388
Gnomad4 AFR exome
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GnomAD4 genome ? Cov.: 35
GnomAD4 genome
?
Cov.:
35
ClinVar
Significance: not provided
Submissions summary: Other:1
Revision: no classification provided
LINK: link
Submissions by phenotype
Phytanic acid storage disease Other:1
not provided, no classification provided | literature only | GeneReviews | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at