GeneBe

rs79957958

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001098512.3(PRKG1):​c.-59_-36delGCCGCCGCCGCCGCCGCCGCCGCC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000798 in 1,253,112 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 0)
Exomes 𝑓: 8.0e-7 ( 0 hom. )

Consequence

PRKG1
NM_001098512.3 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.62

Publications

0 publications found
Variant links:
Genes affected
PRKG1 (HGNC:9414): (protein kinase cGMP-dependent 1) Mammals have three different isoforms of cyclic GMP-dependent protein kinase (Ialpha, Ibeta, and II). These PRKG isoforms act as key mediators of the nitric oxide/cGMP signaling pathway and are important components of many signal transduction processes in diverse cell types. This PRKG1 gene on human chromosome 10 encodes the soluble Ialpha and Ibeta isoforms of PRKG by alternative transcript splicing. A separate gene on human chromosome 4, PRKG2, encodes the membrane-bound PRKG isoform II. The PRKG1 proteins play a central role in regulating cardiovascular and neuronal functions in addition to relaxing smooth muscle tone, preventing platelet aggregation, and modulating cell growth. This gene is most strongly expressed in all types of smooth muscle, platelets, cerebellar Purkinje cells, hippocampal neurons, and the lateral amygdala. Isoforms Ialpha and Ibeta have identical cGMP-binding and catalytic domains but differ in their leucine/isoleucine zipper and autoinhibitory sequences and therefore differ in their dimerization substrates and kinase enzyme activity. [provided by RefSeq, Sep 2011]
PRKG1 Gene-Disease associations (from GenCC):
  • aortic aneurysm, familial thoracic 8
    Inheritance: AD Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
  • familial thoracic aortic aneurysm and aortic dissection
    Inheritance: AD, Unknown Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, ClinGen

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001098512.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
PRKG1
NM_001098512.3
c.-59_-36delGCCGCCGCCGCCGCCGCCGCCGCC
5_prime_UTR
Exon 1 of 18NP_001091982.1Q13976-1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
PRKG1
ENST00000401604.8
TSL:5
c.-59_-36delGCCGCCGCCGCCGCCGCCGCCGCC
5_prime_UTR
Exon 1 of 18ENSP00000384200.4Q13976-1

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
7.98e-7
AC:
1
AN:
1253112
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
617580
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
21802
American (AMR)
AF:
0.00
AC:
0
AN:
23518
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
20292
East Asian (EAS)
AF:
0.00
AC:
0
AN:
28668
South Asian (SAS)
AF:
0.00
AC:
0
AN:
67288
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
44436
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4154
European-Non Finnish (NFE)
AF:
0.00000101
AC:
1
AN:
991636
Other (OTH)
AF:
0.00
AC:
0
AN:
51318
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
2.6

Splicing

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

Publications

Other links and lift over

dbSNP: rs79957958; hg19: chr10-52751070; API