chrX-9684064-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_005647.4(TBL1X):c.233C>T(p.Thr78Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000109 in 1,098,261 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005647.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TBL1X | NM_005647.4 | c.233C>T | p.Thr78Met | missense_variant | Exon 6 of 18 | ENST00000645353.2 | NP_005638.1 | |
TBL1X | NM_001139466.1 | c.233C>T | p.Thr78Met | missense_variant | Exon 6 of 18 | NP_001132938.1 | ||
TBL1X | NM_001139467.1 | c.80C>T | p.Thr27Met | missense_variant | Exon 5 of 17 | NP_001132939.1 | ||
TBL1X | NM_001139468.1 | c.80C>T | p.Thr27Met | missense_variant | Exon 6 of 18 | NP_001132940.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 22
GnomAD3 exomes AF: 0.00000545 AC: 1AN: 183528Hom.: 0 AF XY: 0.0000147 AC XY: 1AN XY: 67954
GnomAD4 exome AF: 0.0000109 AC: 12AN: 1098261Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 2AN XY: 363615
GnomAD4 genome Cov.: 22
ClinVar
Submissions by phenotype
not provided Uncertain:1
This 14 year old male with autism spectrum disorder and moderate intellectual disability was found to carry a maternally inherited missense variant in the TBL1X gene. TBL1X is a gene of uncertain significance; no known human disorders have been clearly associated with this gene. However, deletions of the Xp22.2 to p22.3 region, which includes the TBL1X gene, have been reported in multiple individuals with autism and/or intellectual disability. The patient's mother is reportedly unaffected. The variant is absent from population databases. Computational prediction models are inconsistent. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at