GeneBe

rs886052914

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_002230.4(JUP):​c.*567C>T variant causes a 3 prime UTR 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

JUP
NM_002230.4 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.678

Publications

0 publications found
Variant links:
Genes affected
JUP (HGNC:6207): (junction plakoglobin) This gene encodes a major cytoplasmic protein which is the only known constituent common to submembranous plaques of both desmosomes and intermediate junctions. This protein forms distinct complexes with cadherins and desmosomal cadherins and is a member of the catenin family since it contains a distinct repeating amino acid motif called the armadillo repeat. Mutation in this gene has been associated with Naxos disease. Alternative splicing occurs in this gene; however, not all transcripts have been fully described. [provided by RefSeq, Jul 2008]
JUP Gene-Disease associations (from GenCC):
  • arrhythmogenic right ventricular dysplasia 12
    Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
  • inherited epidermolysis bullosa
    Inheritance: AR Classification: STRONG Submitted by: Genomics England PanelApp
  • Naxos disease
    Inheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Genomics England PanelApp, G2P, Orphanet, PanelApp Australia, Labcorp Genetics (formerly Invitae)
  • lethal acantholytic epidermolysis bullosa
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
JUPNM_002230.4 linkc.*567C>T 3_prime_UTR_variant Exon 14 of 14 ENST00000393931.8 NP_002221.1 P14923A0A0S2Z487

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
JUPENST00000393931.8 linkc.*567C>T 3_prime_UTR_variant Exon 14 of 14 1 NM_002230.4 ENSP00000377508.3 P14923
JUPENST00000310706.9 linkc.*270C>T 3_prime_UTR_variant Exon 15 of 15 1 ENSP00000311113.5 P14923
JUPENST00000393930.5 linkc.*270C>T 3_prime_UTR_variant Exon 15 of 15 5 ENSP00000377507.1 P14923

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
245916
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
124748
African (AFR)
AF:
0.00
AC:
0
AN:
7174
American (AMR)
AF:
0.00
AC:
0
AN:
7434
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
9246
East Asian (EAS)
AF:
0.00
AC:
0
AN:
22906
South Asian (SAS)
AF:
0.00
AC:
0
AN:
2312
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
20890
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
1296
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
158272
Other (OTH)
AF:
0.00
AC:
0
AN:
16386
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
7.2
DANN
Benign
0.40
PhyloP100
0.68
RBP_binding_hub_radar
0.97
RBP_regulation_power_radar
2.3

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

Other links and lift over

dbSNP: rs886052914; hg19: chr17-39911429; API