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GeneBe

3-101682795-T-C

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_000986.4(RPL24):c.305A>G(p.Lys102Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Consequence

RPL24
NM_000986.4 missense

Scores

2
6
11

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 7.96
Variant links:
Genes affected
RPL24 (HGNC:10325): (ribosomal protein L24) 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 L24E family of ribosomal proteins. It is located in the cytoplasm. This gene has been referred to as ribosomal protein L30 because the encoded protein shares amino acid identity with the L30 ribosomal proteins from S. cerevisiae; however, its official name is ribosomal protein L24. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.29846752).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RPL24NM_000986.4 linkuse as main transcriptc.305A>G p.Lys102Arg missense_variant 4/6 ENST00000394077.8
LOC124906262XM_047449411.1 linkuse as main transcriptc.-2484-2100T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RPL24ENST00000394077.8 linkuse as main transcriptc.305A>G p.Lys102Arg missense_variant 4/61 NM_000986.4 P1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
33

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 submitterclinical testingAmbry GeneticsJun 24, 2022The c.305A>G (p.K102R) alteration is located in exon 4 (coding exon 4) of the RPL24 gene. This alteration results from a A to G substitution at nucleotide position 305, causing the lysine (K) at amino acid position 102 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.13
BayesDel_addAF
Uncertain
0.093
D
BayesDel_noAF
Benign
-0.10
Cadd
Uncertain
24
Dann
Uncertain
1.0
DEOGEN2
Benign
0.27
T;T;.
Eigen
Benign
0.11
Eigen_PC
Uncertain
0.26
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Uncertain
0.96
D;D;D
M_CAP
Benign
0.0099
T
MetaRNN
Benign
0.30
T;T;T
MetaSVM
Benign
-0.75
T
MutationAssessor
Uncertain
2.5
M;.;.
MutationTaster
Benign
1.0
D;D;D
PrimateAI
Pathogenic
0.81
D
PROVEAN
Uncertain
-2.5
D;D;D
REVEL
Benign
0.19
Sift
Benign
0.093
T;T;T
Sift4G
Benign
0.14
T;T;T
Polyphen
0.0040
B;B;.
Vest4
0.59
MutPred
0.25
Loss of glycosylation at K102 (P = 0.0355);Loss of glycosylation at K102 (P = 0.0355);Loss of glycosylation at K102 (P = 0.0355);
MVP
0.68
MPC
0.77
ClinPred
0.88
D
GERP RS
5.2
Varity_R
0.37
gMVP
0.31

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr3-101401639; API