20-45891598-CCTGCTGCTGCTGCTGCTGCTGCTGCT-CCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCT
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_000308.4(CTSA):c.45_56dup(p.Leu16_Leu19dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000067 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0000098 ( 0 hom. )
Consequence
CTSA
NM_000308.4 inframe_insertion
NM_000308.4 inframe_insertion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.48
Genes affected
CTSA (HGNC:9251): (cathepsin A) This gene encodes a member of the peptidase S10 family of serine carboxypeptidases. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed to generate two chains that comprise the heterodimeric active enzyme. This enzyme possesses deamidase, esterase and carboxypeptidase activities and acts as a scaffold in the lysosomal multienzyme complex. Mutations in this gene are associated with galactosialidosis. [provided by RefSeq, Nov 2015]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTSA | NM_000308.4 | c.45_56dup | p.Leu16_Leu19dup | inframe_insertion | 2/15 | ENST00000646241.3 | |
CTSA | NM_001127695.3 | c.45_56dup | p.Leu16_Leu19dup | inframe_insertion | 2/15 | ||
CTSA | NM_001167594.3 | c.45_56dup | p.Leu16_Leu19dup | inframe_insertion | 2/14 | ||
CTSA | NR_133656.2 | n.90_101dup | non_coding_transcript_exon_variant | 2/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTSA | ENST00000646241.3 | c.45_56dup | p.Leu16_Leu19dup | inframe_insertion | 2/15 | NM_000308.4 |
Frequencies
GnomAD3 genomes ? AF: 0.00000668 AC: 1AN: 149796Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.00000978 AC: 14AN: 1432032Hom.: 0 Cov.: 0 AF XY: 0.00000561 AC XY: 4AN XY: 712840
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ClinVar
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at