GeneBe

1-110601777-AATATATAT-AATATATATATATATAT

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_004974.4(KCNA2):​c.*1498_*1505dupATATATAT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 22)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

KCNA2
NM_004974.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.61

Publications

0 publications found
Variant links:
Genes affected
KCNA2 (HGNC:6220): (potassium voltage-gated channel subfamily A member 2) Potassium 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, shaker-related subfamily. This member contains six membrane-spanning domains with a shaker-type repeat in the fourth segment. It belongs to the delayed rectifier class, members of which allow nerve cells to efficiently repolarize following an action potential. The coding region of this gene is intronless, and the gene is clustered with genes KCNA3 and KCNA10 on chromosome 1. [provided by RefSeq, Jul 2008]
KCNA2 Gene-Disease associations (from GenCC):
  • developmental and epileptic encephalopathy, 32
    Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
  • genetic developmental and epileptic encephalopathy
    Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
  • undetermined early-onset epileptic encephalopathy
    Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: ClinGen, Orphanet

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 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
KCNA2NM_004974.4 linkc.*1498_*1505dupATATATAT 3_prime_UTR_variant Exon 3 of 3 ENST00000316361.10 NP_004965.1 P16389-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
KCNA2ENST00000316361.10 linkc.*1498_*1505dupATATATAT 3_prime_UTR_variant Exon 3 of 3 2 NM_004974.4 ENSP00000314520.4 P16389-1

Frequencies

GnomAD3 genomes
Cov.:
22
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
850326
Hom.:
0
Cov.:
15
AF XY:
0.00
AC XY:
0
AN XY:
400918
African (AFR)
AF:
0.00
AC:
0
AN:
17276
American (AMR)
AF:
0.00
AC:
0
AN:
6160
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
10180
East Asian (EAS)
AF:
0.00
AC:
0
AN:
18104
South Asian (SAS)
AF:
0.00
AC:
0
AN:
15400
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
11310
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
2186
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
737054
Other (OTH)
AF:
0.00
AC:
0
AN:
32656
GnomAD4 genome
Cov.:
22
Alfa
AF:
0.00
Hom.:
99

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
1.6

Splicing

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

Publications

Other links and lift over

dbSNP: rs149560146; hg19: chr1-111144399; API