rs587777119
Variant names:
Variant summary
Our verdict is Likely pathogenic. The variant received 7 ACMG points: 7P and 0B. PVS1_StrongPM2PP5
The NM_000975.5(RPL11):c.476_477delAA(p.Lys159ArgfsTer12) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
RPL11
NM_000975.5 frameshift
NM_000975.5 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 9.11
Publications
0 publications found
Genes affected
RPL11 (HGNC:10301): (ribosomal protein L11) Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 60S subunit. The protein belongs to the L5P family of ribosomal proteins. It is located in the cytoplasm. The protein probably associates with the 5S rRNA. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. [provided by RefSeq, Dec 2010]
RPL11 Gene-Disease associations (from GenCC):
- Diamond-Blackfan anemia 7Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae), PanelApp Australia
- Diamond-Blackfan anemiaInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
new If you want to explore the variant's impact on the transcript NM_000975.5, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.
ACMG classification
Classification was made for transcript
Our verdict: Likely_pathogenic. The variant received 7 ACMG points.
PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most 50 bp of the penultimate exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.114 CDS is truncated, and there are 3 pathogenic variants in the truncated region.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 1-23695875-CAA-C is Pathogenic according to our data. Variant chr1-23695875-CAA-C is described in ClinVar as Pathogenic. ClinVar VariationId is 100640.Status of the report is no_assertion_criteria_provided, 0 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_000975.5. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| RPL11 | MANE Select | c.476_477delAA | p.Lys159ArgfsTer12 | frameshift | Exon 5 of 6 | ENSP00000496250.1 | P62913-1 | ||
| RPL11 | TSL:1 | c.473_474delAA | p.Lys158ArgfsTer12 | frameshift | Exon 5 of 6 | ENSP00000363676.4 | P62913-2 | ||
| RPL11 | TSL:1 | c.443_444delAA | p.Lys148ArgfsTer12 | frameshift | Exon 4 of 5 | ENSP00000398888.2 | Q5VVC8 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1443970Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 716056
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1443970
Hom.:
AF XY:
AC XY:
0
AN XY:
716056
African (AFR)
AF:
AC:
0
AN:
33260
American (AMR)
AF:
AC:
0
AN:
41934
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25714
East Asian (EAS)
AF:
AC:
0
AN:
39256
South Asian (SAS)
AF:
AC:
0
AN:
82804
European-Finnish (FIN)
AF:
AC:
0
AN:
52224
Middle Eastern (MID)
AF:
AC:
0
AN:
5638
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1103274
Other (OTH)
AF:
AC:
0
AN:
59866
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
ClinVar submissions
View on ClinVar Significance:Pathogenic
Revision:no assertion criteria provided
Pathogenic
VUS
Benign
Condition
1
-
-
Diamond-Blackfan anemia 7 (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.
Publications
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