rs150401343
Positions:
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_001378969.1(KCND3):c.1348C>T(p.Leu450Phe) variant causes a missense change. The variant allele was found at a frequency of 0.0000912 in 1,612,072 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.000072 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000093 ( 0 hom. )
Consequence
KCND3
NM_001378969.1 missense
NM_001378969.1 missense
Scores
7
12
Clinical Significance
Conservation
PhyloP100: 4.93
Genes affected
KCND3 (HGNC:6239): (potassium voltage-gated channel subfamily D member 3) Voltage-gated potassium (Kv) channels represent the most complex class of voltage-gated ion channels from both functional and structural standpoints. Their diverse functions include regulating neurotransmitter release, heart rate, insulin secretion, neuronal excitability, epithelial electrolyte transport, smooth muscle contraction, and cell volume. Four sequence-related potassium channel genes - shaker, shaw, shab, and shal - have been identified in Drosophila, and each has been shown to have human homolog(s). This gene encodes a member of the potassium channel, voltage-gated, shal-related subfamily, members of which form voltage-activated A-type potassium ion channels and are prominent in the repolarization phase of the action potential. This member includes two isoforms with different sizes, which are encoded by alternatively spliced transcript variants of this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PP2
Missense variant in gene, where missense usually causes diseases (based on misZ statistic), KCND3. . Gene score misZ 3.8545 (greater than the threshold 3.09). Trascript score misZ 4.8782 (greater than threshold 3.09). GenCC has associacion of gene with spinocerebellar ataxia type 19/22, Brugada syndrome 1, Brugada syndrome 9.
BP4
Computational evidence support a benign effect (MetaRNN=0.21874768).
BS2
High AC in GnomAd4 at 11 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KCND3 | NM_001378969.1 | c.1348C>T | p.Leu450Phe | missense_variant | 4/8 | ENST00000302127.5 | NP_001365898.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KCND3 | ENST00000302127.5 | c.1348C>T | p.Leu450Phe | missense_variant | 4/8 | 5 | NM_001378969.1 | ENSP00000306923.4 | ||
KCND3 | ENST00000315987.6 | c.1348C>T | p.Leu450Phe | missense_variant | 4/8 | 1 | ENSP00000319591.2 | |||
KCND3 | ENST00000369697.5 | c.1348C>T | p.Leu450Phe | missense_variant | 3/6 | 1 | ENSP00000358711.1 | |||
KCND3 | ENST00000703640.1 | n.2039C>T | non_coding_transcript_exon_variant | 1/3 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152230Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000133 AC: 33AN: 247646Hom.: 0 AF XY: 0.000157 AC XY: 21AN XY: 133642
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GnomAD4 exome AF: 0.0000932 AC: 136AN: 1459724Hom.: 0 Cov.: 32 AF XY: 0.000106 AC XY: 77AN XY: 725754
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GnomAD4 genome AF: 0.0000722 AC: 11AN: 152348Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74498
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:3Uncertain:3Benign:4
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
Brugada syndrome 9 Pathogenic:3
Likely pathogenic, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Apr 09, 2016 | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 01, 2011 | - - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Genomic Research Center, Shahid Beheshti University of Medical Sciences | Dec 03, 2017 | - - |
not provided Uncertain:1Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | KCND3: PP2, BS1 - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 20, 2021 | This variant is associated with the following publications: (PMID: 31130284, 26582918, 22284586, 30609406, 22840528, 21349352, 26016905, 29247119, 28444220, 30662450, 23963749, 30821013) - |
Uncertain significance, no assertion criteria provided | clinical testing | Genetics and Genomic Medicine Centre, NeuroGen Healthcare, NeuroGen Healthcare | Mar 14, 2022 | - - |
Spinocerebellar ataxia type 19/22 Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 11, 2023 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | New York Genome Center | Apr 10, 2021 | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Mendelics | May 04, 2022 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 18, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Benign
DANN
Uncertain
DEOGEN2
Uncertain
.;D;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
.;D;D
M_CAP
Benign
D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L;L
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N
REVEL
Uncertain
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
0.045
.;B;.
Vest4
MVP
MPC
0.96
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at