GeneBe

rs71156237

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The ENST00000301008.5(JPH3):​n.703_732delCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000039 in 1,282,846 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 0.0000039 ( 0 hom. )

Consequence

JPH3
ENST00000301008.5 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.966

Publications

0 publications found
Variant links:
Genes affected
JPH3 (HGNC:14203): (junctophilin 3) Junctional complexes between the plasma membrane and endoplasmic/sarcoplasmic reticulum are a common feature of all excitable cell types and mediate cross talk between cell surface and intracellular ion channels. The protein encoded by this gene is a component of junctional complexes and is composed of a C-terminal hydrophobic segment spanning the endoplasmic/sarcoplasmic reticulum membrane and a remaining cytoplasmic domain that shows specific affinity for the plasma membrane. CAG/CTG repeat expansion from normally 6-28 repeats to 40-59 repeats in the 3' UTR of this gene have been associated with Huntington disease-like 2 (HDL2). This gene is a member of the junctophilin gene family. Alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Jul 2016]
JPH3 Gene-Disease associations (from GenCC):
  • Huntington disease-like 2
    Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, Ambry Genetics

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BS2
High AC in GnomAdExome4 at 5 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
JPH3NM_020655.4 linkc.382+772_382+801delCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG intron_variant Intron 1 of 4 ENST00000284262.3 NP_065706.2 Q8WXH2-1B4DIC1F8W9A3
JPH3NM_001271604.4 linkc.443_472delCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG p.Ala148_Ala157del disruptive_inframe_deletion Exon 2 of 2 NP_001258533.1 F8W9A3Q96HD8
JPH3NM_001271605.3 linkc.*141_*170delCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG 3_prime_UTR_variant Exon 2 of 2 NP_001258534.1 F8W9A3Q96HD8
JPH3NR_073379.3 linkn.96+2370_96+2399delCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG intron_variant Intron 1 of 5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
JPH3ENST00000301008.5 linkn.703_732delCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG non_coding_transcript_exon_variant Exon 2 of 2 1
JPH3ENST00000284262.3 linkc.382+772_382+801delCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG intron_variant Intron 1 of 4 1 NM_020655.4 ENSP00000284262.2 Q8WXH2-1
JPH3ENST00000537256.5 linkn.96+2370_96+2399delCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG intron_variant Intron 1 of 5 2

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
0.00000390
AC:
5
AN:
1282846
Hom.:
0
AF XY:
0.00000474
AC XY:
3
AN XY:
633004
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
28328
American (AMR)
AF:
0.00
AC:
0
AN:
32398
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
21658
East Asian (EAS)
AF:
0.00
AC:
0
AN:
24078
South Asian (SAS)
AF:
0.00
AC:
0
AN:
77828
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
29388
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5062
European-Non Finnish (NFE)
AF:
0.00000494
AC:
5
AN:
1013034
Other (OTH)
AF:
0.00
AC:
0
AN:
51072
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.575
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
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.97

Splicing

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

Publications

Other links and lift over

dbSNP: rs71156237; hg19: chr16-87637893; API