1-55039879-ACTGCTGCTG-ACTGCTGCTGCTGCTGCTGCTG

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BS2_Supporting

The NM_174936.4(PCSK9):​c.54_65dup​(p.Leu20_Leu23dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000456 in 1,557,940 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★). Synonymous variant affecting the same amino acid position (i.e. P14P) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.000059 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000044 ( 0 hom. )

Consequence

PCSK9
NM_174936.4 inframe_insertion

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, multiple submitters, no conflicts U:5

Conservation

PhyloP100: -0.246
Variant links:
Genes affected
PCSK9 (HGNC:20001): (proprotein convertase subtilisin/kexin type 9) This gene encodes a member of the subtilisin-like proprotein convertase family, which includes proteases that process protein and peptide precursors trafficking through regulated or constitutive branches of the secretory pathway. The encoded protein undergoes an autocatalytic processing event with its prosegment in the ER and is constitutively secreted as an inactive protease into the extracellular matrix and trans-Golgi network. It is expressed in liver, intestine and kidney tissues and escorts specific receptors for lysosomal degradation. It plays a role in cholesterol and fatty acid metabolism. Mutations in this gene have been associated with autosomal dominant familial hypercholesterolemia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2014]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -1 ACMG points.

BS2
High AC in GnomAd4 at 9 AD gene. Variant has AC lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PCSK9NM_174936.4 linkuse as main transcriptc.54_65dup p.Leu20_Leu23dup inframe_insertion 1/12 ENST00000302118.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PCSK9ENST00000302118.5 linkuse as main transcriptc.54_65dup p.Leu20_Leu23dup inframe_insertion 1/121 NM_174936.4 P2Q8NBP7-1
PCSK9ENST00000710286.1 linkuse as main transcriptc.411_422dup p.Leu139_Leu142dup inframe_insertion 1/12 A2
PCSK9ENST00000673726.1 linkuse as main transcriptc.54_65dup p.Leu20_Leu23dup inframe_insertion, NMD_transcript_variant 1/6
PCSK9ENST00000673913.2 linkuse as main transcriptc.54_65dup p.Leu20_Leu23dup inframe_insertion, NMD_transcript_variant 1/12

Frequencies

GnomAD3 genomes
AF:
0.0000592
AC:
9
AN:
152070
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0000966
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.0000943
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000588
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000559
AC:
9
AN:
161082
Hom.:
0
AF XY:
0.0000348
AC XY:
3
AN XY:
86248
show subpopulations
Gnomad AFR exome
AF:
0.000115
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.000194
Gnomad NFE exome
AF:
0.0000786
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000441
AC:
62
AN:
1405754
Hom.:
0
Cov.:
30
AF XY:
0.0000374
AC XY:
26
AN XY:
694300
show subpopulations
Gnomad4 AFR exome
AF:
0.000249
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:
0.000245
Gnomad4 NFE exome
AF:
0.0000332
Gnomad4 OTH exome
AF:
0.000103
GnomAD4 genome
AF:
0.0000591
AC:
9
AN:
152186
Hom.:
0
Cov.:
31
AF XY:
0.0000134
AC XY:
1
AN XY:
74422
show subpopulations
Gnomad4 AFR
AF:
0.0000963
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.0000943
Gnomad4 NFE
AF:
0.0000588
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.0000869

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Hypercholesterolemia, autosomal dominant, 3 Uncertain:3
Uncertain significance, criteria provided, single submitterclinical testingFulgent Genetics, Fulgent GeneticsOct 20, 2021- -
Uncertain significance, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 25, 2024This variant, c.54_65dup, results in the insertion of 4 amino acid(s) of the PCSK9 protein (p.Leu20_Leu23dup), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs371488778, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with PCSK9-related conditions. ClinVar contains an entry for this variant (Variation ID: 662731). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Uncertain significance, criteria provided, single submitterclinical testingNew York Genome CenterSep 12, 2022The c.54_65dup variant located in exon 1 of this 12-exon gene is predicted to add four Leucine amino acids [p.(Leu20_Leu23dup)] to a stretch of nine consecutive Leucine amino acids without causing a shift in the reading frame (in-frame duplication). This variant has not been previously reported in the literature and is observedin 36 alleles (0.0071% minor allele frequency with 0 homozygotes) in population databases (gnomAD v2.1.1 and v3.1.2, TOPMed Freeze 8) suggesting it is not a common benign variant in the populations represented in those databases. This variant has been deposited in ClinVar [ClinVar ID: 662731] as a Variant of Uncertain Significance (3 entries). In silico predictions are not available for this variant. Based on available evidence, this c.54_65dup p.(Leu20_Leu23dup) variant identified in PCSK9 is classified as a Variant of Uncertain Significance. -
not provided Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingQuest Diagnostics Nichols Institute San Juan CapistranoJul 11, 2019- -
Familial hypercholesterolemia Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingColor Diagnostics, LLC DBA Color HealthFeb 22, 2023This variant results in an insertion of four leucine residues in a leucine-rich stretch of the PCSK9 protein. To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with PCSK9-related disorders in the literature. This variant has been identified in 14/192344 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -

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.

Other links and lift over

dbSNP: rs35574083; hg19: chr1-55505552; API