rs1553794304
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5
The NM_032898.5(CEP19):c.182_183insA(p.Tyr61Ter) variant causes a stop gained, frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 32)
Consequence
CEP19
NM_032898.5 stop_gained, frameshift
NM_032898.5 stop_gained, frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 5.62
Genes affected
CEP19 (HGNC:28209): (centrosomal protein 19) The protein encoded by this gene localizes to centrosomes and primary cilia and co-localizes with a marker for the mother centriole. This gene resides in a region of human chromosome 3 that is linked to morbid obesity. A homozygous knockout of the orthologous gene in mouse resulted in mice with morbid obesity, hyperphagy, glucose intolerance, and insulin resistance. Mutations in this gene cause morbid obesity and spermatogenic failure (MOSPGF). This gene has a pseudogene on human chromosome 2. [provided by RefSeq, Apr 2014]
PIGX (HGNC:26046): (phosphatidylinositol glycan anchor biosynthesis class X) This gene encodes a type I transmembrane protein in the endoplasmic reticulum (ER). The protein is an essential component of glycosylphosphatidylinositol-mannosyltransferase I, which transfers the first of the four mannoses in the GPI-anchor precursors during GPI-anchor biosynthesis. Studies in rat indicate that the protein is translated from a non-AUG translation initiation site. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 3-196707860-G-GT is Pathogenic according to our data. Variant chr3-196707860-G-GT is described in ClinVar as [Pathogenic]. Clinvar id is 430642.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEP19 | NM_032898.5 | c.182_183insA | p.Tyr61Ter | stop_gained, frameshift_variant | 3/3 | ENST00000409690.5 | |
CEP19 | NM_001379468.1 | c.77_78insA | p.Tyr26Ter | stop_gained, frameshift_variant | 2/2 | ||
CEP19 | NM_001379469.1 | c.182_183insA | p.Tyr61Ter | stop_gained, frameshift_variant | 3/3 | ||
CEP19 | NM_001379470.1 | c.182_183insA | p.Tyr61Ter | stop_gained, frameshift_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEP19 | ENST00000409690.5 | c.182_183insA | p.Tyr61Ter | stop_gained, frameshift_variant | 3/3 | 1 | NM_032898.5 | P1 | |
CEP19 | ENST00000399942.4 | c.77_78insA | p.Tyr26Ter | stop_gained, frameshift_variant | 2/2 | 5 | |||
PIGX | ENST00000426755.5 | c.-11-8997dup | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Cov.: 32
GnomAD4 exome
Cov.:
32
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Bardet-Biedl syndrome Pathogenic:1
Pathogenic, no assertion criteria provided | research | Tolun Lab, Human Genetics Laboratory, Bogazici University | Jul 05, 2017 | it is predicted as truncating, but no further studies were performed. - |
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