rs869025579
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PM4_SupportingPP5_Moderate
The NM_024989.4(PGAP1):c.274_276del(p.Pro92del) 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 Pathogenic (★).
Frequency
Genomes: not found (cov: 32)
Consequence
PGAP1
NM_024989.4 inframe_deletion
NM_024989.4 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 9.23
Genes affected
PGAP1 (HGNC:25712): (post-GPI attachment to proteins inositol deacylase 1) The protein encoded by this gene functions early in the glycosylphosphatidylinositol (GPI) biosynthetic pathway, catalyzing the inositol deacylation of GPI. The encoded protein is required for the production of GPI that can attach to proteins, and this may be an important factor in the transport of GPI-anchored proteins from the endoplasmic reticulum to the Golgi. Defects in this gene are a cause an autosomal recessive form of cognitive impairment. [provided by RefSeq, Jul 2017]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PM4
?
Nonframeshift variant in NON repetitive region in NM_024989.4. Strenght limited to Supporting due to length of the change: 1aa.
PP5
?
Variant 2-196920021-CAGG-C is Pathogenic according to our data. Variant chr2-196920021-CAGG-C is described in ClinVar as [Pathogenic]. Clinvar id is 222979.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-196920021-CAGG-C is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PGAP1 | NM_024989.4 | c.274_276del | p.Pro92del | inframe_deletion | 2/27 | ENST00000354764.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PGAP1 | ENST00000354764.9 | c.274_276del | p.Pro92del | inframe_deletion | 2/27 | 1 | NM_024989.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Cerebral visual impairment and intellectual disability Pathogenic:1
Pathogenic, criteria provided, single submitter | research | Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine | Sep 09, 2015 | This study shows that diverse genetic causes underlie CVI. - |
Intellectual disability, autosomal recessive 42 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | May 24, 2021 | - - |
Computational scores
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Calibrated prediction
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Prediction
Splicing
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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