9-134436505-C-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_002957.6(RXRA):c.1280C>A(p.Ser427Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_002957.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RXRA | NM_002957.6 | c.1280C>A | p.Ser427Tyr | missense_variant | Exon 10 of 10 | ENST00000481739.2 | NP_002948.1 | |
RXRA | NM_001291920.2 | c.1199C>A | p.Ser400Tyr | missense_variant | Exon 10 of 10 | NP_001278849.1 | ||
RXRA | NM_001291921.2 | c.989C>A | p.Ser330Tyr | missense_variant | Exon 9 of 9 | NP_001278850.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RXRA | ENST00000481739.2 | c.1280C>A | p.Ser427Tyr | missense_variant | Exon 10 of 10 | 1 | NM_002957.6 | ENSP00000419692.1 | ||
RXRA | ENST00000672570.1 | c.1199C>A | p.Ser400Tyr | missense_variant | Exon 10 of 10 | ENSP00000500402.1 | ||||
RXRA | ENST00000356384.4 | n.1690C>A | non_coding_transcript_exon_variant | Exon 12 of 12 | 5 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 33
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Pancreatic adenocarcinoma Pathogenic:1
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Transitional cell carcinoma of the bladder Pathogenic:1
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Hepatocellular carcinoma Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at