rs1555423812
Positions:
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_134261.3(RORA):c.804_805del(p.Ser269HisfsTer13) variant causes a frameshift 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 Pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Consequence
RORA
NM_134261.3 frameshift
NM_134261.3 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 7.23
Genes affected
RORA (HGNC:10258): (RAR related orphan receptor A) The protein encoded by this gene is a member of the NR1 subfamily of nuclear hormone receptors. It can bind as a monomer or as a homodimer to hormone response elements upstream of several genes to enhance the expression of those genes. The encoded protein has been shown to interact with NM23-2, a nucleoside diphosphate kinase involved in organogenesis and differentiation, as well as with NM23-1, the product of a tumor metastasis suppressor candidate gene. Also, it has been shown to aid in the transcriptional regulation of some genes involved in circadian rhythm. Four transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Feb 2014]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 12 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 15-60511240-GAC-G is Pathogenic according to our data. Variant chr15-60511240-GAC-G is described in ClinVar as [Pathogenic]. Clinvar id is 549841.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-60511240-GAC-G is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RORA | NM_134261.3 | c.804_805del | p.Ser269HisfsTer13 | frameshift_variant | 5/11 | ENST00000335670.11 | |
RORA-AS1 | NR_120342.1 | n.415+711_415+712del | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RORA | ENST00000335670.11 | c.804_805del | p.Ser269HisfsTer13 | frameshift_variant | 5/11 | 1 | NM_134261.3 | ||
RORA-AS1 | ENST00000559824.5 | n.415+711_415+712del | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:2Other:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Pathogenic:1Other:1
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Nov 21, 2018 | The c.903_904delGT variant in the RORA gene identified in this individual has now been published as a pathogenic variant associated with a RORA-related disorder (Guissart et al., 2018). To our knowledge, this individual represents the only reported individual to harbor this variant. The c.903_904delGT variant causes a frameshift starting with codon Serine 302, changes this amino acid to a Histidine residue, and creates a premature Stop codon at position 13 of the new reading frame, denoted p.Ser302HisfsX13. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.903_904delGT variant is not observed in large population cohorts (Lek et al., 2016). We interpret c.903_904delGT as a pathogenic variant. - |
not provided, no classification provided | phenotyping only | GenomeConnect, ClinGen | - | Variant interpreted as Uncertain significance and reported on 04-24-2017 by Lab or GTR ID 26957. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. - |
Intellectual developmental disorder with or without epilepsy or cerebellar ataxia Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 27, 2018 | - - |
Computational scores
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Calibrated prediction
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Prediction
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at