20-45891598-CCTGCTGCTGCTGCTGCTGCTGCTGCT-CCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCT

Variant names:

• chr20-45891598-C-CCTGCTGCTGCTGCTG
• NM_000308.4:c.42_56dupGCTGCTGCTGCTGCT

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_000308.4(CTSA):​c.42_56dupGCTGCTGCTGCTGCT​(p.Leu15_Leu19dup) variant causes a disruptive 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: not found (cov: 0)
  • Exomes 𝑓: 0.0000028 (0 hom.)
• Consequence: CTSA NM_000308.4 disruptive_inframe_insertion
• 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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CTSA	NM_000308.4	c.42_56dupGCTGCTGCTGCTGCT	p.Leu15_Leu19dup	disruptive_inframe_insertion	Exon 2 of 15	ENST00000646241.3	NP_000299.3
CTSA	NM_001127695.3	c.42_56dupGCTGCTGCTGCTGCT	p.Leu15_Leu19dup	disruptive_inframe_insertion	Exon 2 of 15		NP_001121167.1
CTSA	NM_001167594.3	c.42_56dupGCTGCTGCTGCTGCT	p.Leu15_Leu19dup	disruptive_inframe_insertion	Exon 2 of 14		NP_001161066.2
CTSA	NR_133656.2	n.87_101dupGCTGCTGCTGCTGCT		non_coding_transcript_exon_variant	Exon 2 of 15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CTSA	ENST00000646241.3	c.42_56dupGCTGCTGCTGCTGCT	p.Leu15_Leu19dup	disruptive_inframe_insertion	Exon 2 of 15		NM_000308.4	ENSP00000493613.2

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome AF: 0.00000279 AC: 4 AN: 1432032 Hom.: 0 Cov.: 0 AF XY: 0.00000140 AC XY: 1 AN XY: 712840

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000229

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000274

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr20-44520237;