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GeneBe

3-40462068-C-A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001034996.3(RPL14):c.484C>A(p.Pro162Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 19)

Consequence

RPL14
NM_001034996.3 missense

Scores

1
17

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.35
Variant links:
Genes affected
RPL14 (HGNC:10305): (ribosomal protein L14) 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 L14E family of ribosomal proteins. It contains a basic region-leucine zipper (bZIP)-like domain. The protein is located in the cytoplasm. This gene contains a trinucleotide (GCT) repeat tract whose length is highly polymorphic; these triplet repeats result in a stretch of alanine residues in the encoded protein. Transcript variants utilizing alternative polyA signals and alternative 5'-terminal exons exist but all encode the same protein. 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 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.16956192).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RPL14NM_001034996.3 linkuse as main transcriptc.484C>A p.Pro162Thr missense_variant 6/6 ENST00000396203.7
RPL14NM_003973.5 linkuse as main transcriptc.484C>A p.Pro162Thr missense_variant 6/6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RPL14ENST00000396203.7 linkuse as main transcriptc.484C>A p.Pro162Thr missense_variant 6/61 NM_001034996.3 P1

Frequencies

GnomAD3 genomes
Cov.:
19
GnomAD4 exome
Cov.:
35
GnomAD4 genome
Cov.:
19

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 GeneticsNov 08, 2022The c.484C>A (p.P162T) alteration is located in exon 6 (coding exon 6) of the RPL14 gene. This alteration results from a C to A substitution at nucleotide position 484, causing the proline (P) at amino acid position 162 to be replaced by a threonine (T). 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
0.094
BayesDel_addAF
Benign
-0.067
T
BayesDel_noAF
Benign
-0.33
Cadd
Benign
20
Dann
Benign
0.91
DEOGEN2
Benign
0.080
T;T
Eigen
Benign
-0.38
Eigen_PC
Benign
-0.27
FATHMM_MKL
Benign
0.63
D
M_CAP
Benign
0.022
T
MetaRNN
Benign
0.17
T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
1.6
L;L
MutationTaster
Benign
1.0
D;N;N
PrimateAI
Uncertain
0.55
T
PROVEAN
Benign
-1.3
N;N
REVEL
Benign
0.19
Sift
Benign
0.12
T;T
Sift4G
Benign
0.075
T;T
Polyphen
0.079
B;B
Vest4
0.26
MutPred
0.23
Loss of loop (P = 9e-04);Loss of loop (P = 9e-04);
MVP
0.66
MPC
0.31
ClinPred
0.27
T
GERP RS
3.5
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.079
gMVP
0.070

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: chr3-40503559; API