rs1060500768
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PP2PP3_Strong
The NM_005902.4(SMAD3):c.190T>A(p.Cys64Ser) 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C64R) has been classified as Uncertain significance.
Frequency
Consequence
NM_005902.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMAD3 | NM_005902.4 | c.190T>A | p.Cys64Ser | missense_variant | 1/9 | ENST00000327367.9 | |
SMAD3 | NM_001407011.1 | c.190T>A | p.Cys64Ser | missense_variant | 1/10 | ||
SMAD3 | NM_001407012.1 | c.190T>A | p.Cys64Ser | missense_variant | 1/8 | ||
SMAD3 | NM_001407013.1 | c.190T>A | p.Cys64Ser | missense_variant | 1/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMAD3 | ENST00000327367.9 | c.190T>A | p.Cys64Ser | missense_variant | 1/9 | 1 | NM_005902.4 | P1 | |
SMAD3 | ENST00000560424.2 | c.190T>A | p.Cys64Ser | missense_variant | 1/10 | 3 | |||
SMAD3 | ENST00000559460.6 | c.-110+2400T>A | intron_variant | 4 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 32
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.