11-8038922-G-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_StrongPM2
The NM_003320.5(TUB):c.49G>T(p.Glu17*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,666 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003320.5 stop_gained
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 |
---|---|---|---|---|---|---|---|---|
TUB | NM_003320.5 | c.49G>T | p.Glu17* | stop_gained | Exon 1 of 13 | NP_003311.2 | ||
TUB | XM_005253109.4 | c.164+19564G>T | intron_variant | Intron 1 of 11 | XP_005253166.1 | |||
TUB | XM_047427512.1 | c.164+19564G>T | intron_variant | Intron 1 of 11 | XP_047283468.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TUB | ENST00000305253.8 | c.49G>T | p.Glu17* | stop_gained | Exon 1 of 13 | 1 | ENSP00000305426.4 | |||
TUB | ENST00000534099.5 | c.56+19564G>T | intron_variant | Intron 1 of 11 | 2 | ENSP00000434400.1 | ||||
ENSG00000254921 | ENST00000528151.1 | n.264C>A | non_coding_transcript_exon_variant | Exon 2 of 2 | 4 | |||||
ENSG00000254921 | ENST00000526646.2 | n.202+595C>A | intron_variant | Intron 1 of 1 | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461666Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 727126
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change creates a premature translational stop signal (p.Glu17*) in the TUB gene. It is expected to result in an absent or disrupted protein product. However, the current clinical and genetic evidence is not sufficient to establish whether loss-of-function variants in TUB cause disease. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with TUB-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at