16-87604287-CCTGCTGCTGCTG-C

Position:

• chr16-87604287-CCTGCTGCTGCTG-C

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP3 BS2

The NM_001271604.4(JPH3):​c.461_472delCTGCTGCTGCTG​(p.Ala154_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 0.000614 in 1,432,572 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 0.00091 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00058 (2 hom.)
• Consequence: JPH3 NM_001271604.4 disruptive_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.966

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 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -5 ACMG points.

• BP3: Nonframeshift variant in repetitive region in NM_001271604.4
• BS2: High AC in GnomAd4 at 136 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
JPH3	NM_020655.4	c.382+790_382+801delCTGCTGCTGCTG		intron_variant		ENST00000284262.3	NP_065706.2
JPH3	NM_001271604.4	c.461_472delCTGCTGCTGCTG	p.Ala154_Ala157del	disruptive_inframe_deletion	2/2		NP_001258533.1
JPH3	NM_001271605.3	c.*159_*170delCTGCTGCTGCTG		3_prime_UTR_variant	2/2		NP_001258534.1
JPH3	NR_073379.3	n.96+2388_96+2399delCTGCTGCTGCTG		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
JPH3	ENST00000284262.3	c.382+790_382+801delCTGCTGCTGCTG		intron_variant		1	NM_020655.4	ENSP00000284262.2
JPH3	ENST00000301008.5	n.721_732delCTGCTGCTGCTG		non_coding_transcript_exon_variant	2/2	1
JPH3	ENST00000537256.5	n.96+2388_96+2399delCTGCTGCTGCTG		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.000900 AC: 135 AN: 149956 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00150

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00112

Gnomad ASJ AF: 0.000290

Gnomad EAS AF: 0.000985

Gnomad SAS AF: 0.000636

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.000608

Gnomad OTH AF: 0.00146

GnomAD4 exome AF: 0.000579 AC: 743 AN: 1282508 Hom.: 2 AF XY: 0.000597 AC XY: 378 AN XY: 632830

Gnomad4 AFR exome AF: 0.00194

Gnomad4 AMR exome AF: 0.00117

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.000291

Gnomad4 SAS exome AF: 0.00121

Gnomad4 FIN exome AF: 0.000102

Gnomad4 NFE exome AF: 0.000457

Gnomad4 OTH exome AF: 0.000842

GnomAD4 genome AF: 0.000906 AC: 136 AN: 150064 Hom.: 0 Cov.: 0 AF XY: 0.000819 AC XY: 60 AN XY: 73220

Gnomad4 AFR AF: 0.00152

Gnomad4 AMR AF: 0.00112

Gnomad4 ASJ AF: 0.000290

Gnomad4 EAS AF: 0.000988

Gnomad4 SAS AF: 0.000637

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000608

Gnomad4 OTH AF: 0.00145

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs71156237; hg19: chr16-87637893;