17-42999996-TAC-CAG
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_000988.5(RPL27):c.145_147delinsCAG(p.Tyr49Gln) variant causes a missense 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 Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Consequence
RPL27
NM_000988.5 missense
NM_000988.5 missense
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 9.28
Genes affected
RPL27 (HGNC:10328): (ribosomal protein L27) Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of four RNA species and approximately 80 structurally distinct proteins. This gene encodes a member of the L27e family of ribosomal proteins and a component of the 60S subunit. A splice site mutation in this gene has been identified in a Diamond-Blackfan anemia (DBA) patient. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. [provided by RefSeq, Mar 2017]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
No computational evidence supports a deleterious effect, but strongly conserved according to phyloP
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RPL27 | NM_000988.5 | c.145_147delinsCAG | p.Tyr49Gln | missense_variant | 3/5 | ENST00000253788.12 | NP_000979.1 | |
RPL27 | NM_001349921.2 | c.145_147delinsCAG | p.Tyr49Gln | missense_variant | 3/5 | NP_001336850.1 | ||
RPL27 | NM_001349922.2 | c.145_147delinsCAG | p.Tyr49Gln | missense_variant | 2/4 | NP_001336851.1 | ||
RPL27 | NR_146327.2 | n.136+1165_136+1167delinsCAG | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RPL27 | ENST00000253788.12 | c.145_147delinsCAG | p.Tyr49Gln | missense_variant | 3/5 | 1 | NM_000988.5 | ENSP00000253788 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Nov 02, 2022 | Variant summary: RPL27 c.145_147delinsCAG (p.Tyr49Gln) results in a non-conservative amino acid change located in the Eukaryotic Ribosomal Protein L27, KOW domain (IPR041991) of the encoded protein sequence. Three of four in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251310 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.145_147delinsCAG in individuals affected with Diamond-Blackfan Anemia 16 and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as uncertain significance. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.