chr10-70432959-C-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_018055.5(NODAL):c.1021G>T(p.Val341Leu) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V341M) has been classified as Uncertain significance.
Frequency
Consequence
NM_018055.5 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NODAL | NM_018055.5 | c.1021G>T | p.Val341Leu | missense_variant | 3/3 | ENST00000287139.8 | |
NODAL | NM_001329906.2 | c.622G>T | p.Val208Leu | missense_variant | 3/3 | ||
NODAL | XM_024448028.2 | c.622G>T | p.Val208Leu | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NODAL | ENST00000287139.8 | c.1021G>T | p.Val341Leu | missense_variant | 3/3 | 1 | NM_018055.5 | P1 | |
NODAL | ENST00000414871.1 | c.856G>T | p.Val286Leu | missense_variant | 3/3 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome Cov.: 31
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
congenital heart defects Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Yamagishi Lab, Dept of Pediatrics, Keio University school of medicine | Mar 08, 2023 | only with TBX20 mutation, congenital heart disease occurred - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.