19-50323013-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_004977.3(KCNC3):​c.1940C>G​(p.Pro647Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000716 in 1,396,298 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 7.2e-7 ( 0 hom. )

Consequence

KCNC3
NM_004977.3 missense

Scores

4
11
4

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.98
Variant links:
Genes affected
KCNC3 (HGNC:6235): (potassium voltage-gated channel subfamily C member 3) The Shaker gene family of Drosophila encodes components of voltage-gated potassium channels and is comprised of four subfamilies. Based on sequence similarity, this gene is similar to one of these subfamilies, namely the Shaw subfamily. The protein encoded by this gene belongs to the delayed rectifier class of channel proteins and is an integral membrane protein that mediates the voltage-dependent potassium ion permeability of excitable membranes. Alternate splicing results in several transcript variants. [provided by RefSeq, Mar 2014]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
KCNC3NM_004977.3 linkc.1940C>G p.Pro647Arg missense_variant Exon 2 of 5 ENST00000477616.2 NP_004968.2 Q14003
KCNC3NM_001372305.1 linkc.1712C>G p.Pro571Arg missense_variant Exon 2 of 5 NP_001359234.1
KCNC3NR_110912.2 linkn.69-2229C>G intron_variant Intron 1 of 3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
KCNC3ENST00000477616.2 linkc.1940C>G p.Pro647Arg missense_variant Exon 2 of 5 1 NM_004977.3 ENSP00000434241.1 Q14003
KCNC3ENST00000670667.1 linkc.1940C>G p.Pro647Arg missense_variant Exon 2 of 4 ENSP00000499301.1 A0A590UJ62
KCNC3ENST00000376959.6 linkc.1940C>G p.Pro647Arg missense_variant Exon 2 of 5 5 ENSP00000366158.2 E7ETH1
KCNC3ENST00000474951.1 linkc.-74-2229C>G intron_variant Intron 1 of 3 2 ENSP00000432438.1 E9PQY4

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
7.16e-7
AC:
1
AN:
1396298
Hom.:
0
Cov.:
33
AF XY:
0.00000145
AC XY:
1
AN XY:
688670
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.27e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.51
BayesDel_addAF
Pathogenic
0.22
D
BayesDel_noAF
Uncertain
0.070
CADD
Pathogenic
26
DANN
Uncertain
1.0
DEOGEN2
Benign
0.27
T;T
Eigen
Uncertain
0.34
Eigen_PC
Uncertain
0.26
FATHMM_MKL
Uncertain
0.94
D
LIST_S2
Uncertain
0.97
D;D
M_CAP
Pathogenic
0.61
D
MetaRNN
Uncertain
0.55
D;D
MetaSVM
Pathogenic
0.91
D
MutationAssessor
Uncertain
2.0
.;M
PrimateAI
Pathogenic
0.86
D
PROVEAN
Uncertain
-3.9
D;D
REVEL
Uncertain
0.56
Sift
Benign
0.051
T;D
Sift4G
Benign
0.090
T;T
Polyphen
1.0
D;D
Vest4
0.42
MutPred
0.14
Loss of helix (P = 0.0626);Loss of helix (P = 0.0626);
MVP
0.87
ClinPred
0.96
D
GERP RS
3.1
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.17
gMVP
0.63

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-50826270; API