NM_000288.4:c.12G>A
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_000288.4(PEX7):c.12G>A(p.Val4Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000146 in 1,371,884 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 Likely benign (★).
Frequency
Genomes: not found (cov: 34)
Exomes 𝑓: 0.0000015 ( 0 hom. )
Consequence
PEX7
NM_000288.4 synonymous
NM_000288.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.99
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 -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
Variant 6-136822677-G-A is Benign according to our data. Variant chr6-136822677-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1673677.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.99 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| PEX7 | NM_000288.4 | c.12G>A | p.Val4Val | synonymous_variant | Exon 1 of 10 | ENST00000318471.5 | NP_000279.1 | |
| PEX7 | XM_006715502.3 | c.12G>A | p.Val4Val | synonymous_variant | Exon 1 of 7 | XP_006715565.1 | ||
| PEX7 | XM_047418874.1 | c.12G>A | p.Val4Val | synonymous_variant | Exon 1 of 6 | XP_047274830.1 | ||
| PEX7 | NM_001410945.1 | c.-687G>A | upstream_gene_variant | NP_001397874.1 |
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
34
GnomAD4 exome AF: 0.00000146 AC: 2AN: 1371884Hom.: 0 Cov.: 33 AF XY: 0.00000148 AC XY: 1AN XY: 677114
GnomAD4 exome
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2
AN:
1371884
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33
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1
AN XY:
677114
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GnomAD4 genome
GnomAD4 genome
Cov.:
34
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Peroxisome biogenesis disorder 9B Benign:1
Jul 08, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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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
Publications
No publications associated with this variant yet.