rs200854824
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_001171613.2(PREPL):c.282C>T(p.Thr94Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,662 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. T94T) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Consequence
PREPL
NM_001171613.2 synonymous
NM_001171613.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.736
Publications
0 publications found
Genes affected
PREPL (HGNC:30228): (prolyl endopeptidase like) The protein encoded by this gene belongs to the prolyl oligopeptidase subfamily of serine peptidases. Mutations in this gene have been associated with hypotonia-cystinuria syndrome, also known as the 2p21 deletion syndrome. Several alternatively spliced transcript variants encoding either the same or different isoforms have been described for this gene.[provided by RefSeq, Jan 2010]
PREPL Gene-Disease associations (from GenCC):
- hypotonia-cystinuria syndromeInheritance: AR Classification: STRONG Submitted by: G2P
- myasthenic syndrome, congenital, 22Inheritance: AR Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), PanelApp Australia, Ambry Genetics, Illumina
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BP6
Variant 2-44343812-G-A is Benign according to our data. Variant chr2-44343812-G-A is described in ClinVar as Likely_benign. ClinVar VariationId is 1983566.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.736 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001171613.2. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PREPL | NM_001171613.2 | MANE Select | c.282C>T | p.Thr94Thr | synonymous | Exon 4 of 14 | NP_001165084.1 | ||
| PREPL | NM_001171603.1 | c.549C>T | p.Thr183Thr | synonymous | Exon 5 of 15 | NP_001165074.1 | |||
| PREPL | NM_001171606.2 | c.549C>T | p.Thr183Thr | synonymous | Exon 5 of 15 | NP_001165077.1 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PREPL | ENST00000409411.6 | TSL:1 MANE Select | c.282C>T | p.Thr94Thr | synonymous | Exon 4 of 14 | ENSP00000387095.2 | ||
| PREPL | ENST00000260648.10 | TSL:1 | c.549C>T | p.Thr183Thr | synonymous | Exon 4 of 14 | ENSP00000260648.6 | ||
| PREPL | ENST00000409936.5 | TSL:1 | c.549C>T | p.Thr183Thr | synonymous | Exon 5 of 15 | ENSP00000386543.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD2 exomes AF: 0.00000398 AC: 1AN: 251296 AF XY: 0.00000736 show subpopulations
GnomAD2 exomes
AF:
AC:
1
AN:
251296
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461662Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 727148 show subpopulations
GnomAD4 exome
AF:
AC:
3
AN:
1461662
Hom.:
Cov.:
32
AF XY:
AC XY:
2
AN XY:
727148
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33474
American (AMR)
AF:
AC:
0
AN:
44720
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26132
East Asian (EAS)
AF:
AC:
0
AN:
39686
South Asian (SAS)
AF:
AC:
0
AN:
86256
European-Finnish (FIN)
AF:
AC:
0
AN:
53414
Middle Eastern (MID)
AF:
AC:
0
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
2
AN:
1111824
Other (OTH)
AF:
AC:
1
AN:
60388
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
33
Alfa
AF:
Hom.:
EpiCase
AF:
EpiControl
AF:
ClinVar
ClinVar submissions as Germline
Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
Myasthenic syndrome, congenital, 22 (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
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
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.