rs1555781806
Positions:
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_StrongPP5_Moderate
The NM_004977.3(KCNC3):c.11_12del(p.Ser4CysfsTer96) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Genomes: not found (cov: 20)
Exomes 𝑓: 0.0000018 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
KCNC3
NM_004977.3 frameshift
NM_004977.3 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.17
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 Likely_pathogenic. Variant got 6 ACMG points.
PVS1
?
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant located near the start codon (<100nt), not predicted to undergo nonsense mediated mRNA decay. There are 18 pathogenic variants in the truncated region.
PP5
?
Variant 19-50329070-CTG-C is Pathogenic according to our data. Variant chr19-50329070-CTG-C is described in ClinVar as [Pathogenic]. Clinvar id is 522615.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNC3 | NM_004977.3 | c.11_12del | p.Ser4CysfsTer96 | frameshift_variant | 1/5 | ENST00000477616.2 | |
KCNC3 | NM_001372305.1 | 5_prime_UTR_variant | 1/5 | ||||
KCNC3 | NR_110912.2 | n.68+4397_68+4398del | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNC3 | ENST00000477616.2 | c.11_12del | p.Ser4CysfsTer96 | frameshift_variant | 1/5 | 1 | NM_004977.3 | ||
KCNC3 | ENST00000376959.6 | c.11_12del | p.Ser4CysfsTer96 | frameshift_variant | 1/5 | 5 | A2 | ||
KCNC3 | ENST00000670667.1 | c.11_12del | p.Ser4CysfsTer96 | frameshift_variant | 1/4 | P3 | |||
KCNC3 | ENST00000474951.1 | c.-75+4397_-75+4398del | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 20
GnomAD3 genomes
?
Cov.:
20
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000182 AC: 2AN: 1096650Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 538260
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
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2
AN:
1096650
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0
AN XY:
538260
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GnomAD4 genome ? Cov.: 20
GnomAD4 genome
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Cov.:
20
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Spinocerebellar ataxia type 13 Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Genomic Research Center, Shahid Beheshti University of Medical Sciences | Dec 03, 2017 | - - |
Computational scores
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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