rs193922903

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP3BS2

The NM_001271604.4(JPH3):c.443_472dupCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG(p.Ala148_Ala157dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00059 ( 1 hom., cov: 0)

Exomes 𝑓: 0.00018 ( 7 hom. )

Failed GnomAD Quality Control

Consequence

JPH3
NM_001271604.4 disruptive_inframe_insertion

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:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -5 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_001271604.4

BS2

High AC in GnomAd4 at 88 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
JPH3	NM_020655.4 link	c.382+772_382+801dupCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG		intron_variant	Intron 1 of 4	ENST00000284262.3	NP_065706.2	Q8WXH2-1B4DIC1F8W9A3
JPH3	NM_001271604.4 link	c.443_472dupCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG	p.Ala148_Ala157dup	disruptive_inframe_insertion	Exon 2 of 2		NP_001258533.1	F8W9A3Q96HD8
JPH3	NM_001271605.3 link	c.141_170dupCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG		3_prime_UTR_variant	Exon 2 of 2		NP_001258534.1	F8W9A3Q96HD8
JPH3	NR_073379.3 link	n.96+2370_96+2399dupCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
JPH3	ENST00000284262.3 link	c.382+772_382+801dupCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG	intron_variant	Intron 1 of 4	1	NM_020655.4	ENSP00000284262.2	Q8WXH2-1
JPH3	ENST00000301008.5 link	n.703_732dupCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG	non_coding_transcript_exon_variant	Exon 2 of 2	1
JPH3	ENST00000537256.5 link	n.96+2370_96+2399dupCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG	intron_variant	Intron 1 of 5	2

Frequencies

GnomAD3 genomes

AF:

0.000580

AC:

AN:

149958

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000764

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000595

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000424

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0223

Gnomad NFE

AF:

0.000534

Gnomad OTH

AF:

0.000974

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000179

AC:

229

AN:

1282836

Hom.:

Cov.:

AF XY:

0.000166

AC XY:

105

AN XY:

633000

show subpopulations

Gnomad4 AFR exome

AF:

0.000600

AC:

AN:

28324

Gnomad4 AMR exome

AF:

0.000741

AC:

AN:

32396

Gnomad4 ASJ exome

AF:

0.00

AC:

AN:

21658

Gnomad4 EAS exome

AF:

0.000125

AC:

AN:

24078

Gnomad4 SAS exome

AF:

0.000103

AC:

AN:

77828

Gnomad4 FIN exome

AF:

0.000102

AC:

AN:

29388

Gnomad4 NFE exome

AF:

0.000133

AC:

135

AN:

1013032

Gnomad4 Remaining exome

AF:

0.000431

AC:

AN:

51070

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

<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

AF:

0.000586

AC:

AN:

150066

Hom.:

Cov.:

AF XY:

0.000601

AC XY:

AN XY:

73222

show subpopulations

Gnomad4 AFR

AF:

0.000787

AC:

0.000786859

AN:

0.000786859

Gnomad4 AMR

AF:

0.000594

AC:

0.000594059

AN:

0.000594059

Gnomad4 ASJ

AF:

0.00

AC:

AN:

Gnomad4 EAS

AF:

0.00

AC:

AN:

Gnomad4 SAS

AF:

0.000425

AC:

0.000424628

AN:

0.000424628

Gnomad4 FIN

AF:

0.00

AC:

AN:

Gnomad4 NFE

AF:

0.000534

AC:

0.000533665

AN:

0.000533665

Gnomad4 OTH

AF:

0.000963

AC:

0.000963391

AN:

0.000963391

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

316

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Mutation Taster

=100/0

polymorphism

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