rs797045062
Positions:
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM1PM2PM4_SupportingPP5_Moderate
The NM_004813.4(PEX16):c.995_997del(p.Phe332del) variant causes a inframe deletion change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. F332F) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 33)
Consequence
PEX16
NM_004813.4 inframe_deletion
NM_004813.4 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 8.22
Genes affected
PEX16 (HGNC:8857): (peroxisomal biogenesis factor 16) The protein encoded by this gene is an integral peroxisomal membrane protein. An inactivating nonsense mutation localized to this gene was observed in a patient with Zellweger syndrome of the complementation group CGD/CG9. Expression of this gene product morphologically and biochemically restores the formation of new peroxisomes, suggesting a role in peroxisome organization and biogenesis. Alternative splicing has been observed for this gene and two variants have been described. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
PM1
?
In a region_of_interest Interaction with PEX19 (size 115) in uniprot entity PEX16_HUMAN there are 11 pathogenic changes around while only 0 benign (100%) in NM_004813.4
PM2
?
Very rare variant in population databases, with high coverage;
PM4
?
Nonframeshift variant in NON repetitive region in NM_004813.4. Strenght limited to Supporting due to length of the change: 1aa.
PP5
?
Variant 11-45910267-TAGA-T is Pathogenic according to our data. Variant chr11-45910267-TAGA-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 209181.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PEX16 | NM_004813.4 | c.995_997del | p.Phe332del | inframe_deletion | 11/11 | ENST00000378750.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PEX16 | ENST00000378750.10 | c.995_997del | p.Phe332del | inframe_deletion | 11/11 | 1 | NM_004813.4 | P1 | |
PEX16 | ENST00000241041.7 | c.953-93_953-91del | intron_variant | 1 | |||||
PEX16 | ENST00000532681.5 | c.710_712del | p.Phe237del | inframe_deletion | 11/11 | 3 | |||
PEX16 | ENST00000523721.2 | n.225_227del | non_coding_transcript_exon_variant | 3/3 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Peroxisome biogenesis disorder 8B Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Oct 19, 2012 | Likely pathogenicity based on finding it once in our laboratory homozygous in a 20-year-old female with intellectual disability, spasticity, ataxia, structural brain abnormalities - |
Computational scores
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Calibrated prediction
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Prediction
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