Variant rs758787026 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_145239.3(PRRT2):c.293A>C(p.Asn98Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 31)

Consequence

PRRT2
NM_145239.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0370

Variant links:

Genes affected

PRRT2 (HGNC:30500): (proline rich transmembrane protein 2) This gene encodes a transmembrane protein containing a proline-rich domain in its N-terminal half. Studies in mice suggest that it is predominantly expressed in brain and spinal cord in embryonic and postnatal stages. Mutations in this gene are associated with episodic kinesigenic dyskinesia-1. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]

PRRT2 links:

ENSG00000280893 (HGNC:):

ENSG00000280893 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.03232014).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRRT2	NM_145239.3 linkuse as main transcript	c.293A>C	p.Asn98Thr	missense_variant	2/4	ENST00000358758.12	NP_660282.2	Q7Z6L0-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRRT2	ENST00000358758.12 linkuse as main transcript	c.293A>C	p.Asn98Thr	missense_variant	2/4	1	NM_145239.3	ENSP00000351608.7		Q7Z6L0-1
ENSG00000280893	ENST00000609618.2 linkuse as main transcript	n.293A>C		non_coding_transcript_exon_variant	2/6	5		ENSP00000476774.2		A0A0G2JLL6

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.00000398

AC:

AN:

251260

Hom.:

AF XY:

0.00000736

AC XY:

AN XY:

135816

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000327

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.080

BayesDel_addAF

Benign

-0.30

BayesDel_noAF

Benign

-0.57

CADD

Benign

DANN

Benign

0.68

DEOGEN2

Benign

0.0058

.;.;T;.;T;.;.;.;.;T;.;T;T;.

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.030

LIST_S2

Benign

0.66

T;T;.;.;T;T;T;T;T;.;T;.;T;T

M_CAP

Benign

0.022

MetaRNN

Benign

0.032

T;T;T;T;T;T;T;T;T;T;T;T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.6

.;.;L;L;.;L;.;.;L;L;.;L;L;.

PrimateAI

Benign

0.27

PROVEAN

Benign

-0.32

.;.;N;.;.;N;.;.;N;.;.;.;.;.

REVEL

Benign

0.031

Sift

Benign

0.14

.;.;T;.;.;T;.;.;T;.;.;.;.;.

Sift4G

Benign

0.91

.;T;T;.;.;T;.;.;T;.;.;T;.;.

Polyphen

0.0010, 0.0070

.;.;B;B;.;B;.;.;B;B;.;B;B;.

Vest4

0.21, 0.21, 0.19, 0.21

MutPred

0.18

Gain of glycosylation at N98 (P = 0.0012);Gain of glycosylation at N98 (P = 0.0012);Gain of glycosylation at N98 (P = 0.0012);Gain of glycosylation at N98 (P = 0.0012);Gain of glycosylation at N98 (P = 0.0012);Gain of glycosylation at N98 (P = 0.0012);Gain of glycosylation at N98 (P = 0.0012);Gain of glycosylation at N98 (P = 0.0012);Gain of glycosylation at N98 (P = 0.0012);Gain of glycosylation at N98 (P = 0.0012);Gain of glycosylation at N98 (P = 0.0012);Gain of glycosylation at N98 (P = 0.0012);Gain of glycosylation at N98 (P = 0.0012);Gain of glycosylation at N98 (P = 0.0012);

MVP

0.33

MPC

0.26

ClinPred

0.039

GERP RS

-3.7

Varity_R

0.044

gMVP

0.030

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over