chr3-23917977-C-T

Position:

• chr3-23917977-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_002948.5(RPL15):​c.118C>T​(p.Pro40Ser) 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: RPL15 NM_002948.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 7.86

Genes affected

RPL15 (HGNC:10306): (ribosomal protein L15) 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 L15E family of ribosomal proteins and a component of the 60S subunit. This gene shares sequence similarity with the yeast ribosomal protein YL10 gene. Elevated expression of this gene has been observed in esophageal tumors and gastric cancer tissues, and deletion of this gene has been observed 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]

RPL15 (HGNC:):

NKIRAS1 (HGNC:17899): (NFKB inhibitor interacting Ras like 1) Predicted to enable GTPase activating protein binding activity. Predicted to be involved in I-kappaB kinase/NF-kappaB signaling. Predicted to act upstream of or within several processes, including Ral protein signal transduction; lung alveolus development; and surfactant homeostasis. Located in cytosol and endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.25842762).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RPL15	NM_002948.5	c.118C>T	p.Pro40Ser	missense_variant	2/4	ENST00000307839.10	NP_002939.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RPL15	ENST00000307839.10	c.118C>T	p.Pro40Ser	missense_variant	2/4	1	NM_002948.5	ENSP00000309334.5

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

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Jan 17, 2024

The c.118C>T (p.P40S) alteration is located in exon 2 (coding exon 1) of the RPL15 gene. This alteration results from a C to T substitution at nucleotide position 118, causing the proline (P) at amino acid position 40 to be replaced by a serine (S). 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	Uncertain	0.37
BayesDel_addAF	Uncertain	0.15	D
BayesDel_noAF	Uncertain	-0.020
CADD	Uncertain	24
DANN	Benign	0.90
DEOGEN2	Benign	0.081	T;T;T;T;T;T;.;.;.;T;T;.;T
Eigen	Benign	-0.18
Eigen_PC	Benign	0.0038
FATHMM_MKL	Uncertain	0.97	D
LIST_S2	Uncertain	0.96	.;D;D;D;.;.;D;D;D;.;.;D;.
M_CAP	Benign	0.027	D
MetaRNN	Benign	0.26	T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-0.87	T
MutationAssessor	Benign	0.71	N;.;N;.;N;N;.;N;.;N;N;.;N
PrimateAI	Pathogenic	0.83	D
PROVEAN	Benign	-0.53	N;N;.;N;N;N;.;N;N;N;.;.;N
REVEL	Benign	0.19
Sift	Benign	0.90	T;T;.;T;T;T;.;T;T;T;.;.;T
Sift4G	Benign	0.62	T;T;T;T;T;T;.;T;T;T;.;.;T
Polyphen		0.0020	B;.;B;.;B;B;.;.;.;B;B;.;B
Vest4		0.57
MutPred		0.33		Gain of phosphorylation at P40 (P = 0.0152);Gain of phosphorylation at P40 (P = 0.0152);Gain of phosphorylation at P40 (P = 0.0152);Gain of phosphorylation at P40 (P = 0.0152);Gain of phosphorylation at P40 (P = 0.0152);Gain of phosphorylation at P40 (P = 0.0152);Gain of phosphorylation at P40 (P = 0.0152);Gain of phosphorylation at P40 (P = 0.0152);Gain of phosphorylation at P40 (P = 0.0152);Gain of phosphorylation at P40 (P = 0.0152);Gain of phosphorylation at P40 (P = 0.0152);Gain of phosphorylation at P40 (P = 0.0152);Gain of phosphorylation at P40 (P = 0.0152);
MVP		0.57
MPC		1.5
ClinPred		0.58	D
GERP RS		5.8
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.11
gMVP		0.80

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: chr3-23959468;