9-134417208-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_002957.6(RXRA):​c.661G>C​(p.Glu221Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

RXRA
NM_002957.6 missense

Scores

3
7
9

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 9.50
Variant links:
Genes affected
RXRA (HGNC:10477): (retinoid X receptor alpha) Retinoid X receptors (RXRs) and retinoic acid receptors (RARs) are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors function as transcription factors by binding as homodimers or heterodimers to specific sequences in the promoters of target genes. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, May 2014]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RXRANM_002957.6 linkc.661G>C p.Glu221Gln missense_variant Exon 5 of 10 ENST00000481739.2 NP_002948.1 P19793-1F1D8Q5Q6P3U7
RXRANM_001291920.2 linkc.580G>C p.Glu194Gln missense_variant Exon 5 of 10 NP_001278849.1 A0A5F9ZHH6Q6P3U7
RXRANM_001291921.2 linkc.370G>C p.Glu124Gln missense_variant Exon 4 of 9 NP_001278850.1 P19793-2Q6P3U7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RXRAENST00000481739.2 linkc.661G>C p.Glu221Gln missense_variant Exon 5 of 10 1 NM_002957.6 ENSP00000419692.1 P19793-1
RXRAENST00000672570.1 linkc.580G>C p.Glu194Gln missense_variant Exon 5 of 10 ENSP00000500402.1 A0A5F9ZHH6
RXRAENST00000356384.4 linkn.1071G>C non_coding_transcript_exon_variant Exon 7 of 12 5

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
32

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Feb 05, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.661G>C (p.E221Q) alteration is located in exon 5 (coding exon 5) of the RXRA gene. This alteration results from a G to C substitution at nucleotide position 661, causing the glutamic acid (E) at amino acid position 221 to be replaced by a glutamine (Q). 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
Uncertain
0.53
BayesDel_addAF
Benign
-0.049
T
BayesDel_noAF
Benign
-0.31
CADD
Uncertain
25
DANN
Uncertain
0.99
DEOGEN2
Benign
0.38
T
Eigen
Uncertain
0.41
Eigen_PC
Uncertain
0.32
FATHMM_MKL
Pathogenic
1.0
D
LIST_S2
Pathogenic
0.99
D
M_CAP
Benign
0.034
D
MetaRNN
Uncertain
0.64
D
MetaSVM
Benign
-0.38
T
MutationAssessor
Pathogenic
3.3
M
PrimateAI
Uncertain
0.65
T
PROVEAN
Benign
-2.3
N
REVEL
Benign
0.24
Sift
Uncertain
0.026
D
Sift4G
Benign
0.091
T
Polyphen
0.91
P
Vest4
0.62
MutPred
0.21
Gain of MoRF binding (P = 0.1001);
MVP
0.75
MPC
1.1
ClinPred
0.93
D
GERP RS
3.6
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.51
gMVP
0.63

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: chr9-137309054; API