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GeneBe

19-49491441-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM1

The NM_012423.4(RPL13A):c.419G>A(p.Arg140His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000236 in 127250 control chromosomes in the gnomAD Genomes database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000024 ( 0 hom., cov: 28)
Exomes 𝑓: 0.000013 ( 0 hom. )

Consequence

RPL13A
NM_012423.4 missense

Scores

4
6
5

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 9.63

Links

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM1
?
In a modified_residue Citrulline (size 0) in uniprot entity RL13A_HUMAN

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RPL13ANM_012423.4 linkuse as main transcriptc.419G>A p.Arg140His missense_variant 7/8 ENST00000391857.9
RPL13ANM_001270491.2 linkuse as main transcriptc.236G>A p.Arg79His missense_variant 6/7
RPL13ANR_073024.2 linkuse as main transcriptn.431G>A non_coding_transcript_exon_variant 7/8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RPL13AENST00000391857.9 linkuse as main transcriptc.419G>A p.Arg140His missense_variant 7/81 NM_012423.4 P1

Frequencies

GnomAD3 genomes
AF:
0.0000236
AC:
3
AN:
127250
Hom.:
0
Cov.:
28
show subpopulations
Gnomad AFR
AF:
0.0000604
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000101
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000133
AC:
2
AN:
150546
Hom.:
0
AF XY:
0.0000244
AC XY:
2
AN XY:
81980
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000850
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
ExAC
AF:
0.00000892
AC:
1

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 GeneticsNov 08, 2022The c.419G>A (p.R140H) alteration is located in exon 7 (coding exon 7) of the RPL13A gene. This alteration results from a G to A substitution at nucleotide position 419, causing the arginine (R) at amino acid position 140 to be replaced by a histidine (H). 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
0.91
BayesDel_addAF
Pathogenic
0.27
D
BayesDel_noAF
Pathogenic
0.34
Cadd
Uncertain
24
Dann
Uncertain
1.0
DEOGEN2
Benign
0.18
T;D
Eigen
Uncertain
0.22
Eigen_PC
Uncertain
0.38
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Uncertain
0.88
D;D
M_CAP
Benign
0.029
D
MetaRNN
Uncertain
0.64
D;D
MetaSVM
Benign
-0.73
T
MutationTaster
Benign
1.0
D
PrimateAI
Uncertain
0.79
T
Sift4G
Benign
0.14
T;T
Polyphen
0.032
.;B
Vest4
0.78
MutPred
0.40
.;Loss of MoRF binding (P = 0.0114);
MVP
0.79
MPC
0.59
ClinPred
0.67
D
GERP RS
5.7
Varity_R
0.33
gMVP
0.72

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs754429749; hg19: chr19-49994698; API