rs483352866
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM1PM2PM5PP5
The NM_001199107.2(TBC1D24):āc.533C>Gā(p.Ser178Trp) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,460,950 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S178L) has been classified as Likely pathogenic.
Frequency
Consequence
NM_001199107.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TBC1D24 | NM_001199107.2 | c.533C>G | p.Ser178Trp | missense_variant | 2/8 | ENST00000646147.1 | NP_001186036.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TBC1D24 | ENST00000646147.1 | c.533C>G | p.Ser178Trp | missense_variant | 2/8 | NM_001199107.2 | ENSP00000494678.1 | |||
ENSG00000260272 | ENST00000564543.1 | c.533C>G | p.Ser178Trp | missense_variant | 1/3 | 2 | ENSP00000455547.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1460950Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726854
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
DOORS syndrome Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Institute of Human Genetics, University of Leipzig Medical Center | Jan 01, 2019 | - - |
Developmental and epileptic encephalopathy, 1;C3892048:Autosomal dominant nonsyndromic hearing loss 65;CN236805:Caused by mutation in the TBC1 domain family, member 24 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Apr 18, 2021 | 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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt TBC1D24 protein function. This variant has been observed in individual(s) with autosomal recessive TBC1D24-related conditions (PMID: 27281533). ClinVar contains an entry for this variant (Variation ID: 982832). This variant is not present in population databases (ExAC no frequency). This sequence change replaces serine with tryptophan at codon 178 of the TBC1D24 protein (p.Ser178Trp). The serine residue is highly conserved and there is a large physicochemical difference between serine and tryptophan. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at