chr6-33199270-G-T

Variant summary

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

The NM_021976.5(RXRB):​c.382C>A​(p.Pro128Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000011 in 911,980 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 27)
Exomes 𝑓: 0.0000011 ( 0 hom. )

Consequence

RXRB
NM_021976.5 missense

Scores

5
13

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.96
Variant links:
Genes affected
RXRB (HGNC:10478): (retinoid X receptor beta) This gene encodes a member of the retinoid X receptor (RXR) family of nuclear receptors which are involved in mediating the effects of retinoic acid (RA). The encoded protein forms homodimers with the retinoic acid, thyroid hormone, and vitamin D receptors, increasing both DNA binding and transcriptional function on their respective response elements. This gene lies within the major histocompatibility complex (MHC) class II region on chromosome 6. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jul 2012]

Genome browser will be placed here

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=0.13143).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RXRBNM_021976.5 linkuse as main transcriptc.382C>A p.Pro128Thr missense_variant 2/10 ENST00000374680.4 NP_068811.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RXRBENST00000374680.4 linkuse as main transcriptc.382C>A p.Pro128Thr missense_variant 2/101 NM_021976.5 ENSP00000363812 P4P28702-1
RXRBENST00000374685.8 linkuse as main transcriptc.382C>A p.Pro128Thr missense_variant 2/101 ENSP00000363817 A1P28702-3
RXRBENST00000483281.5 linkuse as main transcriptc.236-806C>A intron_variant, NMD_transcript_variant 5 ENSP00000431369

Frequencies

GnomAD3 genomes
Cov.:
27
GnomAD4 exome
AF:
0.00000110
AC:
1
AN:
911980
Hom.:
0
Cov.:
13
AF XY:
0.00
AC XY:
0
AN XY:
435038
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.0000265
GnomAD4 genome
Cov.:
27
Asia WGS
AF:
0.000289
AC:
1
AN:
3476

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 GeneticsFeb 07, 2023The c.382C>A (p.P128T) alteration is located in exon 2 (coding exon 2) of the RXRB gene. This alteration results from a C to A substitution at nucleotide position 382, causing the proline (P) at amino acid position 128 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
0.068
BayesDel_addAF
Uncertain
0.046
T
BayesDel_noAF
Benign
-0.17
CADD
Benign
18
DANN
Benign
0.84
DEOGEN2
Benign
0.40
.;T
Eigen
Benign
-0.57
Eigen_PC
Benign
-0.46
FATHMM_MKL
Benign
0.56
D
M_CAP
Uncertain
0.22
D
MetaRNN
Benign
0.13
T;T
MetaSVM
Uncertain
-0.23
T
MutationAssessor
Benign
0.90
L;L
MutationTaster
Benign
0.97
D;D;D;D
PrimateAI
Uncertain
0.75
T
PROVEAN
Benign
0.65
N;N
REVEL
Uncertain
0.33
Sift
Benign
0.44
T;T
Sift4G
Benign
0.16
T;T
Polyphen
0.12
.;B
Vest4
0.38
MutPred
0.30
Gain of phosphorylation at P128 (P = 0.0083);Gain of phosphorylation at P128 (P = 0.0083);
MVP
0.46
MPC
0.51
ClinPred
0.54
D
GERP RS
4.2
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.23
gMVP
0.12

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.090
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: rs371739737; hg19: chr6-33167047; API