chr1-206013812-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001910.4(CTSE):c.745C>A(p.Pro249Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,613,632 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000023 ( 0 hom. )
Consequence
CTSE
NM_001910.4 missense
NM_001910.4 missense
Scores
2
5
1
Clinical Significance
Conservation
PhyloP100: 3.49
Genes affected
CTSE (HGNC:2530): (cathepsin E) This gene encodes a member of the A1 family of peptidases. Alternative splicing of this gene results in multiple transcript variants. At least one of these variants encodes a preproprotein that is proteolytically processed to generate the mature enzyme. This enzyme, an aspartic endopeptidase, may be involved in antigen processing and the maturation of secretory proteins. Elevated expression of this gene has been observed in neurodegeneration. [provided by RefSeq, Nov 2015]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTSE | NM_001910.4 | c.745C>A | p.Pro249Thr | missense_variant | 6/9 | ENST00000358184.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTSE | ENST00000358184.7 | c.745C>A | p.Pro249Thr | missense_variant | 6/9 | 1 | NM_001910.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 151914Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251348Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135846
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GnomAD4 exome AF: 0.0000226 AC: 33AN: 1461718Hom.: 0 Cov.: 30 AF XY: 0.0000179 AC XY: 13AN XY: 727162
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 10, 2023 | The c.745C>A (p.P249T) alteration is located in exon 6 (coding exon 6) of the CTSE gene. This alteration results from a C to A substitution at nucleotide position 745, causing the proline (P) at amino acid position 249 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_noAF
Pathogenic
Cadd
Uncertain
Dann
Uncertain
LIST_S2
Uncertain
D;D
MetaRNN
Uncertain
D;D
PROVEAN
Pathogenic
D;D
Sift
Uncertain
D;D
Sift4G
Uncertain
D;D
Vest4
gMVP
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at