1-111780748-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PP2PP3BS2
The NM_001378969.1(KCND3):c.1313C>G(p.Ser438Trp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,613,322 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S438L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001378969.1 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KCND3 | NM_001378969.1 | c.1313C>G | p.Ser438Trp | missense_variant | Exon 4 of 8 | ENST00000302127.5 | NP_001365898.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KCND3 | ENST00000302127.5 | c.1313C>G | p.Ser438Trp | missense_variant | Exon 4 of 8 | 5 | NM_001378969.1 | ENSP00000306923.4 | ||
KCND3 | ENST00000315987.6 | c.1313C>G | p.Ser438Trp | missense_variant | Exon 4 of 8 | 1 | ENSP00000319591.2 | |||
KCND3 | ENST00000369697.5 | c.1313C>G | p.Ser438Trp | missense_variant | Exon 3 of 6 | 1 | ENSP00000358711.1 | |||
KCND3 | ENST00000703640.1 | n.2004C>G | non_coding_transcript_exon_variant | Exon 1 of 3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152178Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461144Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 726716
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152178Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74334
ClinVar
Submissions by phenotype
Spinocerebellar ataxia type 19/22 Uncertain:1
ClinVar contains an entry for this variant (Variation ID: 465164). This sequence change replaces serine, which is neutral and polar, with tryptophan, which is neutral and slightly polar, at codon 438 of the KCND3 protein (p.Ser438Trp). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with KCND3-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. 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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at