rs1172444288
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PM2PP2BS2
The NM_001378969.1(KCND3):c.1313C>T(p.Ser438Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,461,144 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. S438W) 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 -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCND3 | NM_001378969.1 | c.1313C>T | p.Ser438Leu | missense_variant | 4/8 | ENST00000302127.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCND3 | ENST00000302127.5 | c.1313C>T | p.Ser438Leu | missense_variant | 4/8 | 5 | NM_001378969.1 | P3 | |
KCND3 | ENST00000315987.6 | c.1313C>T | p.Ser438Leu | missense_variant | 4/8 | 1 | P3 | ||
KCND3 | ENST00000369697.5 | c.1313C>T | p.Ser438Leu | missense_variant | 3/6 | 1 | A1 | ||
KCND3 | ENST00000703640.1 | n.2004C>T | non_coding_transcript_exon_variant | 1/3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 250026Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135042
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461144Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 726716
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2023 | KCND3: PM2 - |
Uncertain significance, criteria provided, single submitter | clinical testing | Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden | Nov 03, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at