GeneBe

19-45385569-G-A

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7

The NM_006663.4(PPP1R13L):​c.2241C>T​(p.Tyr747Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000686 in 1,458,786 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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: 32)
Exomes 𝑓: 6.9e-7 ( 0 hom. )

Consequence

PPP1R13L
NM_006663.4 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.789

Publications

0 publications found
Variant links:
Genes affected
PPP1R13L (HGNC:18838): (protein phosphatase 1 regulatory subunit 13 like) IASPP is one of the most evolutionarily conserved inhibitors of p53 (TP53; MIM 191170), whereas ASPP1 (MIM 606455) and ASPP2 (MIM 602143) are activators of p53.[supplied by OMIM, Mar 2008]
PPP1R13L Gene-Disease associations (from GenCC):
  • arrhythmogenic cardiomyopathy with variable ectodermal abnormalities
    Inheritance: AR Classification: DEFINITIVE Submitted by: Ambry Genetics
  • dilated cardiomyopathy
    Inheritance: AR Classification: DEFINITIVE Submitted by: G2P

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=-0.5).
BP7
Synonymous conserved (PhyloP=0.789 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PPP1R13LNM_006663.4 linkc.2241C>T p.Tyr747Tyr synonymous_variant Exon 11 of 13 ENST00000360957.10 NP_006654.2 Q8WUF5A0A024R0Q5
PPP1R13LNM_001142502.2 linkc.2241C>T p.Tyr747Tyr synonymous_variant Exon 11 of 13 NP_001135974.1 Q8WUF5A0A024R0Q5
PPP1R13LXM_017026177.2 linkc.2241C>T p.Tyr747Tyr synonymous_variant Exon 12 of 14 XP_016881666.1 Q8WUF5A0A024R0Q5
PPP1R13LXM_017026178.2 linkc.2241C>T p.Tyr747Tyr synonymous_variant Exon 12 of 14 XP_016881667.1 Q8WUF5A0A024R0Q5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PPP1R13LENST00000360957.10 linkc.2241C>T p.Tyr747Tyr synonymous_variant Exon 11 of 13 1 NM_006663.4 ENSP00000354218.4 Q8WUF5

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
6.86e-7
AC:
1
AN:
1458786
Hom.:
0
Cov.:
32
AF XY:
0.00000138
AC XY:
1
AN XY:
725472
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
33438
American (AMR)
AF:
0.00
AC:
0
AN:
44636
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
26048
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39666
South Asian (SAS)
AF:
0.00
AC:
0
AN:
86120
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
52402
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5714
European-Non Finnish (NFE)
AF:
9.00e-7
AC:
1
AN:
1110534
Other (OTH)
AF:
0.00
AC:
0
AN:
60228
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
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
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.50
CADD
Benign
8.8
DANN
Benign
0.96
PhyloP100
0.79
PromoterAI
0.10
Neutral

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

Other links and lift over

dbSNP: rs1114167453; hg19: chr19-45888827; COSMIC: COSV62910025; COSMIC: COSV62910025; API