chr6-7402846-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_031480.3(RIOK1):c.716C>T(p.Pro239Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,613,540 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 Uncertain significance (★).
Frequency
Consequence
NM_031480.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RIOK1 | NM_031480.3 | c.716C>T | p.Pro239Leu | missense_variant | Exon 8 of 17 | ENST00000379834.7 | NP_113668.2 | |
RIOK1 | NM_001348194.2 | c.404C>T | p.Pro135Leu | missense_variant | Exon 8 of 17 | NP_001335123.1 | ||
RIOK1 | XM_011514933.4 | c.752C>T | p.Pro251Leu | missense_variant | Exon 8 of 17 | XP_011513235.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RIOK1 | ENST00000379834.7 | c.716C>T | p.Pro239Leu | missense_variant | Exon 8 of 17 | 1 | NM_031480.3 | ENSP00000369162.2 | ||
RIOK1 | ENST00000475351.5 | n.*460C>T | splice_region_variant, non_coding_transcript_exon_variant | Exon 8 of 8 | 1 | ENSP00000418263.1 | ||||
RIOK1 | ENST00000475351.5 | n.*460C>T | 3_prime_UTR_variant | Exon 8 of 8 | 1 | ENSP00000418263.1 | ||||
RIOK1 | ENST00000264874.7 | n.401C>T | non_coding_transcript_exon_variant | Exon 4 of 13 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152002Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461538Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727052
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152002Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74240
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.716C>T (p.P239L) alteration is located in exon 8 (coding exon 8) of the RIOK1 gene. This alteration results from a C to T substitution at nucleotide position 716, causing the proline (P) at amino acid position 239 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at