rs104894381
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1PM2PM5PP3_StrongPP5
The NM_181486.4(TBX5):c.238G>A(p.Gly80Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 13/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G80E) has been classified as Likely pathogenic.
Frequency
Consequence
NM_181486.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBX5 | NM_181486.4 | c.238G>A | p.Gly80Arg | missense_variant | 3/9 | ENST00000405440.7 | |
TBX5 | NM_000192.3 | c.238G>A | p.Gly80Arg | missense_variant | 3/9 | ||
TBX5 | NM_080717.4 | c.88G>A | p.Gly30Arg | missense_variant | 2/8 | ||
TBX5 | XM_017019912.2 | c.286G>A | p.Gly96Arg | missense_variant | 3/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBX5 | ENST00000405440.7 | c.238G>A | p.Gly80Arg | missense_variant | 3/9 | 1 | NM_181486.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome Cov.: 31
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Holt-Oram syndrome Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 16, 1999 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at