chr22-37051800-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001282684.2(KCTD17):c.40G>T(p.Ala14Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A14V) has been classified as Uncertain significance.
Frequency
Consequence
NM_001282684.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCTD17 | NM_001282684.2 | c.40G>T | p.Ala14Ser | missense_variant | 1/9 | ENST00000403888.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCTD17 | ENST00000403888.8 | c.40G>T | p.Ala14Ser | missense_variant | 1/9 | 1 | NM_001282684.2 | A2 | |
KCTD17 | ENST00000402077.8 | c.40G>T | p.Ala14Ser | missense_variant | 1/8 | 1 | A2 | ||
KCTD17 | ENST00000610767.5 | c.40G>T | p.Ala14Ser | missense_variant | 1/6 | 3 | P2 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1111608Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 532764
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
Myoclonic dystonia 26 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Apr 26, 2023 | 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. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant  is likely to be tolerated. This variant has not been reported in the literature in individuals affected with KCTD17-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces alanine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 21 of the KCTD17 protein (p.Ala21Ser). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at