6-112079638-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_016262.5(TUBE1):c.443G>A(p.Gly148Glu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,459,522 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016262.5 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TUBE1 | NM_016262.5 | c.443G>A | p.Gly148Glu | missense_variant | Exon 6 of 12 | ENST00000368662.10 | NP_057346.1 | |
TUBE1 | XM_047418854.1 | c.311G>A | p.Gly104Glu | missense_variant | Exon 5 of 11 | XP_047274810.1 | ||
TUBE1 | XM_047418855.1 | c.218G>A | p.Gly73Glu | missense_variant | Exon 4 of 10 | XP_047274811.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249114Hom.: 0 AF XY: 0.00000743 AC XY: 1AN XY: 134656
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1459522Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 725982
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.443G>A (p.G148E) alteration is located in exon 6 (coding exon 6) of the TUBE1 gene. This alteration results from a G to A substitution at nucleotide position 443, causing the glycine (G) at amino acid position 148 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at