NM_015001.3:c.359C>G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_015001.3(SPEN):c.359C>G(p.Pro120Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015001.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPEN | ENST00000375759.8 | c.359C>G | p.Pro120Arg | missense_variant | Exon 2 of 15 | 1 | NM_015001.3 | ENSP00000364912.3 | ||
SPEN | ENST00000673875.1 | c.155C>G | p.Pro52Arg | missense_variant | Exon 3 of 12 | ENSP00000501122.1 | ||||
SPEN | ENST00000438066.2 | n.359C>G | non_coding_transcript_exon_variant | Exon 2 of 15 | 3 | ENSP00000388021.2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Radio-Tartaglia syndrome Uncertain:1
The p.Pro120Arg variant in the SPEN gene has not been previously reported in association with disease. This variant was absent from large population databases, including the Genome Aggregation Database (http://gnomad.broadinstitute.org/). In silico tools predict that p.Pro120Arg variant in SPEN does not impact protein function; however, these predictions have not been tested directly. Using ACMG guidelines, this variant was classified as a variant of uncertain significance (ACMG evidence codes used: PM2_supporting, BP4). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.