GeneBe

rs3217229

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP3

The NM_001289104.2(PRKCSH):​c.951_968delGGAGGAGGAGGAGGAGGA​(p.Glu318_Glu323del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0000067 ( 0 hom., cov: 0)

Consequence

PRKCSH
NM_001289104.2 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.27

Publications

11 publications found
Variant links:
Genes affected
PRKCSH (HGNC:9411): (PRKCSH beta subunit of glucosidase II) This gene encodes the beta-subunit of glucosidase II, an N-linked glycan-processing enzyme in the endoplasmic reticulum. The encoded protein is an acidic phosphoprotein known to be a substrate for protein kinase C. Mutations in this gene have been associated with the autosomal dominant polycystic liver disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]
PRKCSH Gene-Disease associations (from GenCC):
  • polycystic liver disease 1
    Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), ClinGen, Ambry Genetics, Orphanet, Genomics England PanelApp

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -1 ACMG points.

BP3
Nonframeshift variant in repetitive region in NM_001289104.2

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PRKCSHNM_001289104.2 linkc.951_968delGGAGGAGGAGGAGGAGGA p.Glu318_Glu323del disruptive_inframe_deletion Exon 11 of 18 ENST00000677123.1 NP_001276033.1 K7ELL7B4DJQ5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PRKCSHENST00000677123.1 linkc.951_968delGGAGGAGGAGGAGGAGGA p.Glu318_Glu323del disruptive_inframe_deletion Exon 11 of 18 NM_001289104.2 ENSP00000503163.1 K7ELL7

Frequencies

GnomAD3 genomes
AF:
0.00000669
AC:
1
AN:
149518
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000663
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.00000669
AC:
1
AN:
149518
Hom.:
0
Cov.:
0
AF XY:
0.0000137
AC XY:
1
AN XY:
72784
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
40504
American (AMR)
AF:
0.0000663
AC:
1
AN:
15074
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3436
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5066
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4684
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10162
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
67356
Other (OTH)
AF:
0.00
AC:
0
AN:
2030
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
0.00
Hom.:
370

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
3.3
Mutation Taster
=135/65
polymorphism

Splicing

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

Publications

Other links and lift over

dbSNP: rs3217229; hg19: chr19-11558340; API