16-81139583-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The ENST00000525539.5(PKD1L2):c.5547G>T(p.Arg1849Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000422 in 1,422,420 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000042 ( 0 hom. )
Consequence
PKD1L2
ENST00000525539.5 missense
ENST00000525539.5 missense
Scores
1
1
Clinical Significance
Conservation
PhyloP100: -0.466
Genes affected
PKD1L2 (HGNC:21715): (polycystin 1 like 2 (gene/pseudogene)) This gene encodes a member of the polycystin protein family. This protein may function as a G-protein-coupled component or regulator of cation channel pores. The long isoform of this protein contains 11 transmembrane domains, a latrophilin/CL-1-like GPCR proteolytic site (GPS) domain, and a polycystin-1, lipoxygenase, alpha-toxin (PLAT) domain. Alternative splicing results in multiple transcript variants encoding distinct isoforms. This gene is a polymorphic pseudogene in humans. [provided by RefSeq, May 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.17).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PKD1L2 | NR_126532.3 | n.5562G>T | non_coding_transcript_exon_variant | 32/43 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PKD1L2 | ENST00000525539.5 | c.5547G>T | p.Arg1849Ser | missense_variant | 32/43 | 1 | |||
PKD1L2 | ENST00000533478.5 | c.3492G>T | p.Arg1164Ser | missense_variant | 21/32 | 1 | |||
PKD1L2 | ENST00000530363.5 | n.203+1714G>T | intron_variant, non_coding_transcript_variant | 1 | |||||
PKD1L2 | ENST00000299598.11 | n.4944G>T | non_coding_transcript_exon_variant | 22/25 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
GnomAD3 exomes AF: 0.0000268 AC: 5AN: 186530Hom.: 0 AF XY: 0.0000100 AC XY: 1AN XY: 99770
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GnomAD4 exome AF: 0.00000422 AC: 6AN: 1422420Hom.: 0 Cov.: 66 AF XY: 0.00000142 AC XY: 1AN XY: 703644
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GnomAD4 genome ? Cov.: 33
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33
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 11, 2022 | The c.5547G>T (p.R1849S) alteration is located in exon 32 (coding exon 32) of the PKD1L2 gene. This alteration results from a G to T substitution at nucleotide position 5547, causing the arginine (R) at amino acid position 1849 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at