rs149455886

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_006917.5(RXRG):​c.182C>T​(p.Thr61Ile) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T61N) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)

Consequence

RXRG
NM_006917.5 missense

Scores

7
12

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.99
Variant links:
Genes affected
RXRG (HGNC:10479): (retinoid X receptor gamma) This gene encodes a member of the retinoid X receptor (RXR) family of nuclear receptors which are involved in mediating the antiproliferative effects of retinoic acid (RA). This receptor forms dimers with the retinoic acid, thyroid hormone, and vitamin D receptors, increasing both DNA binding and transcriptional function on their respective response elements. This gene is expressed at significantly lower levels in non-small cell lung cancer cells. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jun 2010]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.2873744).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RXRGNM_006917.5 linkc.182C>T p.Thr61Ile missense_variant Exon 2 of 10 ENST00000359842.10 NP_008848.1 P48443F1D8Q7
RXRGNM_001256570.2 linkc.-246C>T 5_prime_UTR_variant Exon 2 of 11 NP_001243499.1 A0A087WZ88F1T097

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RXRGENST00000359842.10 linkc.182C>T p.Thr61Ile missense_variant Exon 2 of 10 1 NM_006917.5 ENSP00000352900.5 P48443
RXRGENST00000619224.1 linkc.-246C>T 5_prime_UTR_variant Exon 2 of 11 1 ENSP00000482458.1 A0A087WZ88

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
33
Bravo
AF:
0.0000113
ESP6500AA
AF:
0.000227
AC:
1
ESP6500EA
AF:
0.00
AC:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.087
BayesDel_addAF
Benign
0.0056
T
BayesDel_noAF
Benign
-0.23
CADD
Uncertain
23
DANN
Uncertain
1.0
DEOGEN2
Benign
0.35
T
Eigen
Benign
0.048
Eigen_PC
Benign
0.21
FATHMM_MKL
Uncertain
0.90
D
LIST_S2
Benign
0.85
D
M_CAP
Benign
0.052
D
MetaRNN
Benign
0.29
T
MetaSVM
Uncertain
-0.15
T
MutationAssessor
Benign
0.0
N
PrimateAI
Uncertain
0.60
T
PROVEAN
Benign
-0.96
N
REVEL
Uncertain
0.30
Sift
Uncertain
0.0020
D
Sift4G
Uncertain
0.054
T
Polyphen
0.32
B
Vest4
0.31
MVP
0.38
MPC
0.076
ClinPred
0.77
D
GERP RS
4.7
Varity_R
0.18
gMVP
0.58

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: rs149455886; hg19: chr1-165398071; API