rs1554335937
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PVS1_StrongPM2PP5_Moderate
The NM_000288.4(PEX7):c.871_874del(p.Gly291Ter) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,459,598 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. C290C) has been classified as Likely benign.
Frequency
Consequence
NM_000288.4 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PEX7 | NM_000288.4 | c.871_874del | p.Gly291Ter | frameshift_variant | 9/10 | ENST00000318471.5 | |
PEX7 | NM_001410945.1 | c.757_760del | p.Gly253Ter | frameshift_variant | 9/10 | ||
PEX7 | XM_006715502.3 | c.577_580del | p.Gly193Ter | frameshift_variant | 6/7 | ||
PEX7 | XM_047418874.1 | c.594_597del | p.Val199ArgfsTer? | frameshift_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PEX7 | ENST00000318471.5 | c.871_874del | p.Gly291Ter | frameshift_variant | 9/10 | 1 | NM_000288.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1459598Hom.: 0 AF XY: 0.00000275 AC XY: 2AN XY: 726328
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Rhizomelic chondrodysplasia punctata type 1 Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Counsyl | May 24, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at