rs79087668

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_153026.3(PRICKLE1):​c.370G>C​(p.Ala124Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,842 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A124T) has been classified as Benign.

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 6.8e-7 ( 0 hom. )

Consequence

PRICKLE1
NM_153026.3 missense

Scores

16
3

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.95
Variant links:
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]

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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 rank MANE Protein UniProt
PRICKLE1NM_153026.3 linkc.370G>C p.Ala124Pro missense_variant Exon 4 of 8 ENST00000345127.9 NP_694571.2 Q96MT3A0A024R0W7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PRICKLE1ENST00000345127.9 linkc.370G>C p.Ala124Pro missense_variant Exon 4 of 8 1 NM_153026.3 ENSP00000345064.3 Q96MT3

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461842
Hom.:
0
Cov.:
32
AF XY:
0.00000138
AC XY:
1
AN XY:
727228
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
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:
8.99e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.39
BayesDel_addAF
Uncertain
0.13
D
BayesDel_noAF
Uncertain
-0.040
CADD
Benign
23
DANN
Uncertain
1.0
DEOGEN2
Benign
0.41
T;T;T;T;T;T;T;T;T;T;T;.
Eigen
Uncertain
0.33
Eigen_PC
Uncertain
0.32
FATHMM_MKL
Uncertain
0.95
D
LIST_S2
Uncertain
0.91
.;.;.;.;.;.;.;.;.;D;D;D
M_CAP
Benign
0.085
D
MetaRNN
Uncertain
0.73
D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM
Uncertain
-0.042
T
MutationAssessor
Uncertain
2.6
M;M;M;M;M;M;M;M;M;M;.;.
PrimateAI
Uncertain
0.51
T
PROVEAN
Uncertain
-2.4
N;.;N;.;N;.;.;N;.;N;D;.
REVEL
Uncertain
0.38
Sift
Uncertain
0.0090
D;.;D;.;D;.;.;D;.;D;T;.
Sift4G
Uncertain
0.014
D;.;D;.;D;.;.;D;.;D;.;.
Polyphen
0.82
P;P;P;P;P;P;P;P;P;P;.;.
Vest4
0.76
MutPred
0.61
Loss of MoRF binding (P = 0.0627);Loss of MoRF binding (P = 0.0627);Loss of MoRF binding (P = 0.0627);Loss of MoRF binding (P = 0.0627);Loss of MoRF binding (P = 0.0627);Loss of MoRF binding (P = 0.0627);Loss of MoRF binding (P = 0.0627);Loss of MoRF binding (P = 0.0627);Loss of MoRF binding (P = 0.0627);Loss of MoRF binding (P = 0.0627);Loss of MoRF binding (P = 0.0627);Loss of MoRF binding (P = 0.0627);
MVP
0.73
MPC
0.46
ClinPred
0.88
D
GERP RS
3.5
Varity_R
0.66
gMVP
0.63

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: chr12-42863266; API