1-24533174-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_013441.4(RCAN3):c.461C>T(p.Pro154Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000331 in 1,607,300 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_013441.4 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 |
---|---|---|---|---|---|---|---|---|
RCAN3 | NM_013441.4 | c.461C>T | p.Pro154Leu | missense_variant | Exon 4 of 5 | ENST00000374395.9 | NP_038469.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000164 AC: 25AN: 152180Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000224 AC: 55AN: 245096Hom.: 0 AF XY: 0.000241 AC XY: 32AN XY: 132782
GnomAD4 exome AF: 0.000348 AC: 507AN: 1455120Hom.: 0 Cov.: 34 AF XY: 0.000330 AC XY: 239AN XY: 723950
GnomAD4 genome AF: 0.000164 AC: 25AN: 152180Hom.: 0 Cov.: 33 AF XY: 0.0000942 AC XY: 7AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.461C>T (p.P154L) alteration is located in exon 4 (coding exon 3) of the RCAN3 gene. This alteration results from a C to T substitution at nucleotide position 461, causing the proline (P) at amino acid position 154 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