GeneBe

rs193922903

Positions:

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_020655.4(JPH3):​c.382+778_382+801dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000142 in 1,432,888 control chromosomes in the GnomAD database, including 2 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00044 ( 0 hom., cov: 0)
Exomes 𝑓: 0.00011 ( 2 hom. )

Consequence

JPH3
NM_020655.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.966
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2
High AC in GnomAd4 at 66 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
JPH3NM_020655.4 linkuse as main transcriptc.382+778_382+801dup intron_variant ENST00000284262.3
JPH3NM_001271604.4 linkuse as main transcriptc.449_472dup p.Ala150_Ala157dup inframe_insertion 2/2
JPH3NM_001271605.3 linkuse as main transcriptc.*147_*170dup 3_prime_UTR_variant 2/2
JPH3NR_073379.3 linkuse as main transcriptn.96+2376_96+2399dup intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
JPH3ENST00000284262.3 linkuse as main transcriptc.382+778_382+801dup intron_variant 1 NM_020655.4 P1Q8WXH2-1
JPH3ENST00000301008.5 linkuse as main transcriptn.709_732dup non_coding_transcript_exon_variant 2/21
JPH3ENST00000537256.5 linkuse as main transcriptn.96+2376_96+2399dup intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.000420
AC:
63
AN:
149958
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00106
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000463
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000788
Gnomad SAS
AF:
0.000424
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000741
Gnomad OTH
AF:
0.000974
GnomAD4 exome
AF:
0.000107
AC:
137
AN:
1282822
Hom.:
2
Cov.:
30
AF XY:
0.000103
AC XY:
65
AN XY:
632992
show subpopulations
Gnomad4 AFR exome
AF:
0.000459
Gnomad4 AMR exome
AF:
0.000247
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00166
Gnomad4 SAS exome
AF:
0.000283
Gnomad4 FIN exome
AF:
0.000170
Gnomad4 NFE exome
AF:
0.0000365
Gnomad4 OTH exome
AF:
0.000215
GnomAD4 genome
AF:
0.000440
AC:
66
AN:
150066
Hom.:
0
Cov.:
0
AF XY:
0.000396
AC XY:
29
AN XY:
73222
show subpopulations
Gnomad4 AFR
AF:
0.00111
Gnomad4 AMR
AF:
0.000462
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000790
Gnomad4 SAS
AF:
0.000425
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000741
Gnomad4 OTH
AF:
0.00145

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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.

Other links and lift over

dbSNP: rs71156237; hg19: chr16-87637893; API