GeneBe

rs371775061

Variant names:

Variant summary

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

The NM_001042475.3(CEP85L):​c.1020+6883_1020+6902delGTGTGTGTGTGTGTGTGTGT variant causes a intron 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 0.0000090 ( 0 hom., cov: 0)

Consequence

CEP85L
NM_001042475.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.379

Publications

0 publications found
Variant links:
Genes affected
CEP85L (HGNC:21638): (centrosomal protein 85 like) The protein encoded by this gene was identified as a breast cancer antigen. Nothing more is known of its function at this time. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2010]
PLN (HGNC:9080): (phospholamban) The protein encoded by this gene is found as a pentamer and is a major substrate for the cAMP-dependent protein kinase in cardiac muscle. The encoded protein is an inhibitor of cardiac muscle sarcoplasmic reticulum Ca(2+)-ATPase in the unphosphorylated state, but inhibition is relieved upon phosphorylation of the protein. The subsequent activation of the Ca(2+) pump leads to enhanced muscle relaxation rates, thereby contributing to the inotropic response elicited in heart by beta-agonists. The encoded protein is a key regulator of cardiac diastolic function. Mutations in this gene are a cause of inherited human dilated cardiomyopathy with refractory congestive heart failure, and also familial hypertrophic cardiomyopathy. [provided by RefSeq, Apr 2016]
PLN Gene-Disease associations (from GenCC):
  • dilated cardiomyopathy 1P
    Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), G2P
  • intrinsic cardiomyopathy
    Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
  • hypertrophic cardiomyopathy 18
    Inheritance: AD Classification: STRONG, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), PanelApp Australia
  • arrhythmogenic right ventricular cardiomyopathy
    Inheritance: AD Classification: MODERATE Submitted by: ClinGen
  • familial isolated dilated cardiomyopathy
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

Genome browser will be placed here

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_001042475.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
CEP85L
NM_001042475.3
MANE Select
c.1020+6883_1020+6902delGTGTGTGTGTGTGTGTGTGT
intron
N/ANP_001035940.1Q5SZL2-1
PLN
NM_002667.5
MANE Select
c.-97-183_-97-164delCACACACACACACACACACA
intron
N/ANP_002658.1P26678
CEP85L
NM_001178035.2
c.1029+6883_1029+6902delGTGTGTGTGTGTGTGTGTGT
intron
N/ANP_001171506.1Q5SZL2-4

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
CEP85L
ENST00000368491.8
TSL:1 MANE Select
c.1020+6883_1020+6902delGTGTGTGTGTGTGTGTGTGT
intron
N/AENSP00000357477.3Q5SZL2-1
PLN
ENST00000357525.6
TSL:1 MANE Select
c.-97-198_-97-179delACACACACACACACACACAC
intron
N/AENSP00000350132.5P26678
CEP85L
ENST00000434604.5
TSL:1
c.1029+6883_1029+6902delGTGTGTGTGTGTGTGTGTGT
intron
N/AENSP00000392131.1A2A3P3

Frequencies

GnomAD3 genomes
AF:
0.00000896
AC:
1
AN:
111604
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00
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:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000189
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.00000896
AC:
1
AN:
111604
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
52164
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
30772
American (AMR)
AF:
0.00
AC:
0
AN:
11126
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
2874
East Asian (EAS)
AF:
0.00
AC:
0
AN:
4008
South Asian (SAS)
AF:
0.00
AC:
0
AN:
2636
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
4776
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
226
European-Non Finnish (NFE)
AF:
0.0000189
AC:
1
AN:
52962
Other (OTH)
AF:
0.00
AC:
0
AN:
1484
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.575
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.:
143

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.38

Splicing

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

Publications

Other links and lift over

dbSNP: rs371775061; hg19: chr6-118879789; API