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GeneBe

19-49490790-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2_SupportingPP3

The NM_012423.4(RPL13A):c.268C>T(p.His90Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD Genomes project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Consequence

RPL13A
NM_012423.4 missense

Scores

7
3
5

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 7.46

Links

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
?
Very rare variant; Number of alleles below threshold, Median coverage is 33.
PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.767

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RPL13ANM_012423.4 linkuse as main transcriptc.268C>T p.His90Tyr missense_variant 5/8 ENST00000391857.9
RPL13ANM_001270491.2 linkuse as main transcriptc.85C>T p.His29Tyr missense_variant 4/7
RPL13ANR_073024.2 linkuse as main transcriptn.280C>T non_coding_transcript_exon_variant 5/8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RPL13AENST00000391857.9 linkuse as main transcriptc.268C>T p.His90Tyr missense_variant 5/81 NM_012423.4 P1

Frequencies

GnomAD3 genomes
Cov.:
33

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsAug 02, 2022The c.268C>T (p.H90Y) alteration is located in exon 5 (coding exon 5) of the RPL13A gene. This alteration results from a C to T substitution at nucleotide position 268, causing the histidine (H) at amino acid position 90 to be replaced by a tyrosine (Y). 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
Pathogenic
0.88
BayesDel_addAF
Pathogenic
0.26
D
BayesDel_noAF
Uncertain
0.13
Cadd
Uncertain
26
Dann
Uncertain
1.0
DEOGEN2
Benign
0.15
T;D
Eigen
Pathogenic
0.71
Eigen_PC
Pathogenic
0.73
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Uncertain
0.95
D;D
M_CAP
Benign
0.017
T
MetaRNN
Pathogenic
0.77
D;D
MetaSVM
Benign
-0.47
T
MutationTaster
Benign
1.0
D
PrimateAI
Pathogenic
0.83
D
Sift4G
Benign
0.16
T;T
Polyphen
0.99
.;D
Vest4
0.82
MutPred
0.60
.;Loss of methylation at K91 (P = 0.0587);
MVP
0.57
MPC
1.4
ClinPred
0.99
D
GERP RS
5.7
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.73
gMVP
0.83

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: chr19-49994047; API