rs750077647

Variant names:

• chr4-88008021-CGAGGAGGAG-C
• NM_000297.4:c.299_307delAGGAGGAGG

Your query was ambiguous. Multiple possible variants found:

• chr4-88008021-CGAGGAGGAG-C
• chr4-88008021-CGAGGAGGAG-CGAG
• chr4-88008021-CGAGGAGGAG-CGAGGAG
• chr4-88008021-CGAGGAGGAG-CGAGGAGGAGGAG
• chr4-88008021-CGAGGAGGAG-CGAGGAGGAGGAGGAG
• chr4-88008021-CGAGGAGGAG-CGAGGAGGAGGAGGAGGAG

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_000297.4(PKD2):​c.299_307delAGGAGGAGG​(p.Glu100_Glu102del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.000000732 in 1,366,202 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 7.3e-7 (0 hom.)
• Consequence: PKD2 NM_000297.4 disruptive_inframe_deletion
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 4.36

Genes affected

PKD2 (HGNC:9009): (polycystin 2, transient receptor potential cation channel) This gene encodes a member of the polycystin protein family. The encoded protein is a multi-pass membrane protein that functions as a calcium permeable cation channel, and is involved in calcium transport and calcium signaling in renal epithelial cells. This protein interacts with polycystin 1, and they may be partners in a common signaling cascade involved in tubular morphogenesis. Mutations in this gene are associated with autosomal dominant polycystic kidney disease type 2. [provided by RefSeq, Mar 2011]

ENSG00000286618 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PKD2	NM_000297.4	c.299_307delAGGAGGAGG	p.Glu100_Glu102del	disruptive_inframe_deletion	Exon 1 of 15	ENST00000237596.7	NP_000288.1
PKD2	XM_011532028.3	c.299_307delAGGAGGAGG	p.Glu100_Glu102del	disruptive_inframe_deletion	Exon 1 of 14		XP_011530330.1
PKD2	NR_156488.2	n.398_406delAGGAGGAGG		non_coding_transcript_exon_variant	Exon 1 of 14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PKD2	ENST00000237596.7	c.299_307delAGGAGGAGG	p.Glu100_Glu102del	disruptive_inframe_deletion	Exon 1 of 15	1	NM_000297.4	ENSP00000237596.2
ENSG00000286618	ENST00000662475.1	n.112+336_112+344delCTCCTCCTC		intron_variant	Intron 1 of 2
PKD2	ENST00000506727.1	n.-210_-202delGAGGAGGAG		upstream_gene_variant		4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 7.32e-7 AC: 1 AN: 1366202 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 673980

Gnomad4 AFR exome AF: 0.0000331

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Polycystic kidney disease 2 Uncertain:1

Mar 11, 2024

Fulgent Genetics, Fulgent Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr4-88929173;