19-54206364-G-T

Variant names:

• chr19-54206364-G-T
• rs201691172
• NM_001013.4:c.309G>T

Variant summary

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

The NM_001013.4(RPS9):​c.309G>T​(p.Glu103Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: RPS9 NM_001013.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.720

Genes affected

RPS9 (HGNC:10442): (ribosomal protein S9) 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 40S subunit. The protein belongs to the S4P family of ribosomal proteins. It is located in the cytoplasm. Variable expression of this gene in colorectal cancers compared to adjacent normal tissues has been observed, although no correlation between the level of expression and the severity of the disease has been found. As is typical for genes encoding ribosomal proteins, multiple processed pseudogenes derived from this gene are 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 rank	MANE	Protein	UniProt
RPS9	NM_001013.4	c.309G>T	p.Glu103Asp	missense_variant	Exon 4 of 5	ENST00000302907.9	NP_001004.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPS9	ENST00000302907.9	c.309G>T	p.Glu103Asp	missense_variant	Exon 4 of 5	1	NM_001013.4	ENSP00000302896.4

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.54
BayesDel_addAF	Uncertain	0.057	T
BayesDel_noAF	Benign	-0.16
CADD	Benign	23
DANN	Uncertain	1.0
DEOGEN2	Benign	0.32	T;T;T;T;T;T
Eigen	Benign	-0.044
Eigen_PC	Benign	0.0023
FATHMM_MKL	Uncertain	0.89	D
M_CAP	Benign	0.052	D
MetaRNN	Uncertain	0.47	T;T;T;T;T;T
MetaSVM	Benign	-0.85	T
MutationAssessor	Pathogenic	3.0	M;.;M;.;M;.
PrimateAI	Pathogenic	0.88	D
PROVEAN	Benign	-1.7	N;.;N;N;N;N
REVEL	Benign	0.26
Sift	Uncertain	0.019	D;.;D;D;D;D
Sift4G	Benign	0.063	T;T;T;T;T;T
Polyphen		0.0010	B;B;B;B;B;B
Vest4		0.77
MutPred		0.56		Gain of ubiquitination at K101 (P = 0.1204);Gain of ubiquitination at K101 (P = 0.1204);Gain of ubiquitination at K101 (P = 0.1204);Gain of ubiquitination at K101 (P = 0.1204);Gain of ubiquitination at K101 (P = 0.1204);Gain of ubiquitination at K101 (P = 0.1204);
MVP		0.89
MPC		1.4
ClinPred		0.96	D
GERP RS		2.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.27
gMVP		0.93

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

LitVar

Other links and lift over

dbSNP: rs201691172; hg19: chr19-54710232;