14-44962496-CA-C
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PVS1_StrongPM2PP5_Moderate
The NM_001308120.2(TOGARAM1):c.76delA(p.Ser26ValfsTer17) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★).
Frequency
Consequence
NM_001308120.2 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TOGARAM1 | NM_001308120.2 | c.76delA | p.Ser26ValfsTer17 | frameshift_variant | Exon 1 of 20 | ENST00000361462.7 | NP_001295049.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Joubert syndrome 37 Pathogenic:1
The observed frameshift c.76delp.Ser26ValfsTer17 variant in TOGARAM1 gene has not been reported previously as a pathogenic variant nor a benign variant, to our knowledge. The p.Ser26ValfsTer17 variant is absent in gnomAD Exomes. This variant has not been submitted to the ClinVar database. This variant causes a frameshift starting with codon Serine 26, changes this amino acid to Valine residue, and creates a premature Stop codon at position 17 of the new reading frame, denoted p.Ser26ValfsTer17. This variant is predicted to cause loss of normal protein function through protein truncation. Loss of function variants have been previously reported to be disease causing. For these reasons, this variant has been classified as Likely Pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.