rs2084385144
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP4
The NM_024663.4(NPEPL1):c.59G>C(p.Arg20Pro) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
NPEPL1
NM_024663.4 missense
NM_024663.4 missense
Scores
2
2
14
Clinical Significance
Conservation
PhyloP100: 3.65
Publications
0 publications found
Genes affected
NPEPL1 (HGNC:16244): (aminopeptidase like 1) Predicted to enable manganese ion binding activity and metalloaminopeptidase activity. Predicted to be involved in proteolysis. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
STX16-NPEPL1 (HGNC:41993): (STX16-NPEPL1 readthrough (NMD candidate)) This locus represents naturally occurring read-through transcription between the neighboring syntaxin 16 (STX16) and aminopeptidase-like 1 (NPEPL1) genes on chromosome 20. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is thus unlikely to produce a protein product. [provided by RefSeq, Mar 2011]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.28508908).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_024663.4. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| NPEPL1 | TSL:1 MANE Select | c.59G>C | p.Arg20Pro | missense | Exon 1 of 12 | ENSP00000348395.6 | Q8NDH3-1 | ||
| NPEPL1 | TSL:1 | c.67-778G>C | intron | N/A | ENSP00000434810.1 | Q8NDH3-4 | |||
| STX16-NPEPL1 | TSL:5 | n.*134-778G>C | intron | N/A | ENSP00000457522.1 | H3BU86 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1040116Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 504848
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1040116
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
504848
African (AFR)
AF:
AC:
0
AN:
20050
American (AMR)
AF:
AC:
0
AN:
14890
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
13564
East Asian (EAS)
AF:
AC:
0
AN:
15908
South Asian (SAS)
AF:
AC:
0
AN:
45480
European-Finnish (FIN)
AF:
AC:
0
AN:
15438
Middle Eastern (MID)
AF:
AC:
0
AN:
2988
European-Non Finnish (NFE)
AF:
AC:
0
AN:
874670
Other (OTH)
AF:
AC:
0
AN:
37128
GnomAD4 genome
GnomAD4 genome
Cov.:
32
Alfa
AF:
Hom.:
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Benign
T
M_CAP
Uncertain
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
PhyloP100
PrimateAI
Pathogenic
D
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
D
Vest4
MutPred
Gain of glycosylation at R20 (P = 0.0075)
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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