8-144792101-T-C

Position:

• chr8-144792101-T-C

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001317782.2(RPL8):​c.29A>G​(p.Lys10Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000000696 in 1,437,632 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 7.0e-7 (0 hom.)
• Consequence: RPL8 NM_001317782.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 4.86

Genes affected

RPL8 (HGNC:10368): (ribosomal protein L8) 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 L2P family of ribosomal proteins. It is located in the cytoplasm. In rat, the protein associates with the 5.8S rRNA, very likely participates in the binding of aminoacyl-tRNA, and is a constituent of the elongation factor 2-binding site at the ribosomal subunit interface. Alternatively spliced transcript variants encoding the same protein exist. 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]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RPL8	NM_001317782.2	c.29A>G	p.Lys10Arg	missense_variant	1/5	ENST00000528957.6	NP_001304711.1
RPL8	NM_000973.5	c.29A>G	p.Lys10Arg	missense_variant	2/6		NP_000964.1
RPL8	NM_001317771.2	c.29A>G	p.Lys10Arg	missense_variant	2/6		NP_001304700.1
RPL8	NM_033301.3	c.29A>G	p.Lys10Arg	missense_variant	2/6		NP_150644.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RPL8	ENST00000528957.6	c.29A>G	p.Lys10Arg	missense_variant	1/5	1	NM_001317782.2	ENSP00000433464.2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 6.96e-7 AC: 1 AN: 1437632 Hom.: 0 Cov.: 32 AF XY: 0.00000140 AC XY: 1 AN XY: 714468

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.0000168

GnomAD4 genome Cov.: 33

Bravo AF: 0.00000756

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Oct 13, 2023

The c.29A>G (p.K10R) alteration is located in exon 2 (coding exon 1) of the RPL8 gene. This alteration results from a A to G substitution at nucleotide position 29, causing the lysine (K) at amino acid position 10 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	0.19
BayesDel_addAF	Benign	-0.11	T
BayesDel_noAF	Benign	-0.39
CADD	Pathogenic	26
DANN	Uncertain	0.99
DEOGEN2	Benign	0.077	T;T;T;T;.;T
Eigen	Benign	0.089
Eigen_PC	Uncertain	0.22
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Pathogenic	0.98	.;D;.;D;D;D
M_CAP	Benign	0.0058	T
MetaRNN	Uncertain	0.43	T;T;T;T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Uncertain	2.8	M;.;M;M;.;.
PrimateAI	Pathogenic	0.91	D
PROVEAN	Uncertain	-2.6	D;N;D;N;N;N
REVEL	Benign	0.15
Sift	Uncertain	0.029	D;D;D;D;D;D
Sift4G	Benign	0.89	T;T;T;T;.;T
Polyphen		0.45	P;.;P;P;.;.
Vest4		0.60
MutPred		0.29		Loss of ubiquitination at K10 (P = 0.0381);Loss of ubiquitination at K10 (P = 0.0381);Loss of ubiquitination at K10 (P = 0.0381);Loss of ubiquitination at K10 (P = 0.0381);Loss of ubiquitination at K10 (P = 0.0381);Loss of ubiquitination at K10 (P = 0.0381);
MVP		0.68
MPC		0.79
ClinPred		0.89	D
GERP RS		5.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.56
gMVP		0.69

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1234028238; hg19: chr8-146017486;