chr12-42460619-A-C
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_153026.3(PRICKLE1):c.1686T>G(p.Ser562Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,460,646 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 (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
PRICKLE1
NM_153026.3 synonymous
NM_153026.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0190
Publications
0 publications found
Genes affected
PRICKLE1 (HGNC:17019): (prickle planar cell polarity protein 1) This gene encodes a nuclear receptor that may be a negative regulator of the Wnt/beta-catenin signaling pathway. The encoded protein localizes to the nuclear membrane and has been implicated in the nuclear trafficking of the transcription repressors REST/NRSF and REST4. Mutations in this gene have been linked to progressive myoclonus epilepsy. Alternate splicing results in multiple transcript variants. A pseudogene of this gene is found on chromosome 3. [provided by RefSeq, Sep 2009]
PRICKLE1 Gene-Disease associations (from GenCC):
- epilepsy, progressive myoclonic, 1BInheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
- Unverricht-Lundborg syndromeInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- progressive myoclonus epilepsyInheritance: AR Classification: LIMITED Submitted by: ClinGen
- epilepsyInheritance: AD Classification: NO_KNOWN Submitted by: ClinGen
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.65).
BP6
Variant 12-42460619-A-C is Benign according to our data. Variant chr12-42460619-A-C is described in CliVar as Likely_benign. Clinvar id is 537248.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-42460619-A-C is described in CliVar as Likely_benign. Clinvar id is 537248.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-42460619-A-C is described in CliVar as Likely_benign. Clinvar id is 537248.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-42460619-A-C is described in CliVar as Likely_benign. Clinvar id is 537248.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-42460619-A-C is described in CliVar as Likely_benign. Clinvar id is 537248.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-42460619-A-C is described in CliVar as Likely_benign. Clinvar id is 537248.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-42460619-A-C is described in CliVar as Likely_benign. Clinvar id is 537248.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-42460619-A-C is described in CliVar as Likely_benign. Clinvar id is 537248.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-42460619-A-C is described in CliVar as Likely_benign. Clinvar id is 537248.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-42460619-A-C is described in CliVar as Likely_benign. Clinvar id is 537248.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-42460619-A-C is described in CliVar as Likely_benign. Clinvar id is 537248.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-42460619-A-C is described in CliVar as Likely_benign. Clinvar id is 537248.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-42460619-A-C is described in CliVar as Likely_benign. Clinvar id is 537248.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-42460619-A-C is described in CliVar as Likely_benign. Clinvar id is 537248.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-42460619-A-C is described in CliVar as Likely_benign. Clinvar id is 537248.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-42460619-A-C is described in CliVar as Likely_benign. Clinvar id is 537248.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-42460619-A-C is described in CliVar as Likely_benign. Clinvar id is 537248.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-42460619-A-C is described in CliVar as Likely_benign. Clinvar id is 537248.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-42460619-A-C is described in CliVar as Likely_benign. Clinvar id is 537248.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-42460619-A-C is described in CliVar as Likely_benign. Clinvar id is 537248.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-42460619-A-C is described in CliVar as Likely_benign. Clinvar id is 537248.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-42460619-A-C is described in CliVar as Likely_benign. Clinvar id is 537248.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-42460619-A-C is described in CliVar as Likely_benign. Clinvar id is 537248.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-42460619-A-C is described in CliVar as Likely_benign. Clinvar id is 537248.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-42460619-A-C is described in CliVar as Likely_benign. Clinvar id is 537248.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-42460619-A-C is described in CliVar as Likely_benign. Clinvar id is 537248.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-42460619-A-C is described in CliVar as Likely_benign. Clinvar id is 537248.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-42460619-A-C is described in CliVar as Likely_benign. Clinvar id is 537248.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-42460619-A-C is described in CliVar as Likely_benign. Clinvar id is 537248.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-42460619-A-C is described in CliVar as Likely_benign. Clinvar id is 537248.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-42460619-A-C is described in CliVar as Likely_benign. Clinvar id is 537248.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-42460619-A-C is described in CliVar as Likely_benign. Clinvar id is 537248.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-42460619-A-C is described in CliVar as Likely_benign. Clinvar id is 537248.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-42460619-A-C is described in CliVar as Likely_benign. Clinvar id is 537248.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-42460619-A-C is described in CliVar as Likely_benign. Clinvar id is 537248.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.019 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| PRICKLE1 | NM_153026.3 | c.1686T>G | p.Ser562Ser | synonymous_variant | Exon 8 of 8 | ENST00000345127.9 | NP_694571.2 |
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460646Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 726680 show subpopulations
GnomAD4 exome
AF:
AC:
2
AN:
1460646
Hom.:
Cov.:
33
AF XY:
AC XY:
0
AN XY:
726680
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33480
American (AMR)
AF:
AC:
0
AN:
44722
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26136
East Asian (EAS)
AF:
AC:
2
AN:
39700
South Asian (SAS)
AF:
AC:
0
AN:
86258
European-Finnish (FIN)
AF:
AC:
0
AN:
52202
Middle Eastern (MID)
AF:
AC:
0
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1111988
Other (OTH)
AF:
AC:
0
AN:
60392
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Epilepsy, progressive myoclonic, 1B Benign:1
Oct 28, 2023
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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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