18-26455780-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001142730.3(KCTD1):c.2561C>T(p.Pro854Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000316 in 1,613,958 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. P854S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001142730.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCTD1 | NM_001142730.3 | c.2561C>T | p.Pro854Leu | missense_variant | 5/5 | ENST00000580059.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCTD1 | ENST00000580059.7 | c.2561C>T | p.Pro854Leu | missense_variant | 5/5 | 3 | NM_001142730.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152114Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251400Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135872
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1461844Hom.: 0 Cov.: 32 AF XY: 0.0000289 AC XY: 21AN XY: 727224
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152114Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74306
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 10, 2023 | The c.2561C>T (p.P854L) alteration is located in exon 5 (coding exon 5) of the KCTD1 gene. This alteration results from a C to T substitution at nucleotide position 2561, causing the proline (P) at amino acid position 854 to be replaced by a leucine (L). 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