chr9-4827019-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PM4PP5
The NM_005772.5(RCL1):c.370C>T(p.Gln124Ter) variant causes a stop gained change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,614,050 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_005772.5 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RCL1 | NM_005772.5 | c.370C>T | p.Gln124Ter | stop_gained | 3/9 | ENST00000381750.9 | |
RCL1 | NM_001286699.2 | c.-90-6135C>T | intron_variant | ||||
RCL1 | NM_001286700.2 | c.-91+3400C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RCL1 | ENST00000381750.9 | c.370C>T | p.Gln124Ter | stop_gained | 3/9 | 1 | NM_005772.5 | P1 | |
RCL1 | ENST00000381732.3 | c.370C>T | p.Gln124Ter | stop_gained | 3/3 | 2 | |||
RCL1 | ENST00000442869.5 | c.-91+3400C>T | intron_variant | 3 | |||||
RCL1 | ENST00000473230.1 | n.213+3400C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152168Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461882Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727242
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74334
ClinVar
Submissions by phenotype
Psychotic disorder Pathogenic:1
Pathogenic, no assertion criteria provided | clinical testing | Gene Discovery Core-Manton Center, Boston Children's Hospital | Nov 05, 2020 | ENST00000381750.4:c.370C>T, p.Gln124Ter, 370/1122 results in a premature truncation of the protein and thus scored as Pathogenic using ACMG criteria. It is absent from controls. However, there are limited functional studies on RCL1 at this time and the carrier father has a less severe behavioral phenotype. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at