Variant 16-87604287-CCTGCTGCTGCTGCTGCTGCTGCTGCTG-CCTGCTG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP3BP6BS2

The NM_001271604.4(JPH3):c.452_472delCTGCTGCTGCTGCTGCTGCTG(p.Ala151_Ala157del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000403 in 1,432,822 control chromosomes in the GnomAD database, including 5 homozygotes. Variant has been reported in Lovd as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.00067 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00037 ( 5 hom. )

Consequence

JPH3
NM_001271604.4 disruptive_inframe_deletion

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]

JPH3 links:

JPH3 (HGNC:):

JPH3 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_001271604.4

BP6

Variant 16-87604287-CCTGCTGCTGCTGCTGCTGCTG-C is Benign according to our data. Variant chr16-87604287-CCTGCTGCTGCTGCTGCTGCTG-C is described in Lovd as [Likely_benign].

BS2

High AC in GnomAd4 at 101 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
JPH3	NM_020655.4 linkuse as main transcript	c.382+781_382+801delCTGCTGCTGCTGCTGCTGCTG		intron_variant		ENST00000284262.3	NP_065706.2	Q8WXH2-1B4DIC1F8W9A3
JPH3	NM_001271604.4 linkuse as main transcript	c.452_472delCTGCTGCTGCTGCTGCTGCTG	p.Ala151_Ala157del	disruptive_inframe_deletion	2/2		NP_001258533.1	F8W9A3Q96HD8
JPH3	NM_001271605.3 linkuse as main transcript	c.150_170delCTGCTGCTGCTGCTGCTGCTG		3_prime_UTR_variant	2/2		NP_001258534.1	F8W9A3Q96HD8
JPH3	NR_073379.3 linkuse as main transcript	n.96+2379_96+2399delCTGCTGCTGCTGCTGCTGCTG		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
JPH3	ENST00000284262.3 linkuse as main transcript	c.382+781_382+801delCTGCTGCTGCTGCTGCTGCTG	intron_variant		1	NM_020655.4	ENSP00000284262.2	Q8WXH2-1
JPH3	ENST00000301008.5 linkuse as main transcript	n.712_732delCTGCTGCTGCTGCTGCTGCTG	non_coding_transcript_exon_variant	2/2	1
JPH3	ENST00000537256.5 linkuse as main transcript	n.96+2379_96+2399delCTGCTGCTGCTGCTGCTGCTG	intron_variant		2

Frequencies

GnomAD3 genomes

AF:

0.000674

AC:

101

AN:

149958

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000173

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000132

Gnomad ASJ

AF:

0.0145

Gnomad EAS

AF:

0.000197

Gnomad SAS

AF:

0.00106

Gnomad FIN

AF:

0.000388

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000445

Gnomad OTH

AF:

0.000974

GnomAD4 exome

AF:

0.000372

AC:

477

AN:

1282756

Hom.:

AF XY:

0.000355

AC XY:

225

AN XY:

632940

show subpopulations

Gnomad4 AFR exome

AF:

0.000106

Gnomad4 AMR exome

AF:

0.0000926

Gnomad4 ASJ exome

AF:

0.00846

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000180

Gnomad4 FIN exome

AF:

0.000272

Gnomad4 NFE exome

AF:

0.000227

Gnomad4 OTH exome

AF:

0.000666

GnomAD4 genome

AF:

0.000673

AC:

101

AN:

150066

Hom.:

Cov.:

AF XY:

0.000656

AC XY:

AN XY:

73222

show subpopulations

Gnomad4 AFR

AF:

0.000172

Gnomad4 AMR

AF:

0.000132

Gnomad4 ASJ

AF:

0.0145

Gnomad4 EAS

AF:

0.000198

Gnomad4 SAS

AF:

0.00106

Gnomad4 FIN

AF:

0.000388

Gnomad4 NFE

AF:

0.000445

Gnomad4 OTH

AF:

0.000963

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.

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