rs1242600338

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM4BS2

The NM_021614.4(KCNN2):​c.428_439delACGCGCAGCAGT​(p.Tyr143_Gln146del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.0000391 in 460,938 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: 33)
Exomes 𝑓: 0.000039 ( 0 hom. )

Consequence

KCNN2
NM_021614.4 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.06
Variant links:
Genes affected
KCNN2 (HGNC:6291): (potassium calcium-activated channel subfamily N member 2) Action potentials in vertebrate neurons are followed by an afterhyperpolarization (AHP) that may persist for several seconds and may have profound consequences for the firing pattern of the neuron. Each component of the AHP is kinetically distinct and is mediated by different calcium-activated potassium channels. The protein encoded by this gene is activated before membrane hyperpolarization and is thought to regulate neuronal excitability by contributing to the slow component of synaptic AHP. This gene is a member of the KCNN family of potassium channel genes. The encoded protein is an integral membrane protein that forms a voltage-independent calcium-activated channel with three other calmodulin-binding subunits. Alternate splicing of this gene results in multiple transcript variants. [provided by RefSeq, May 2013]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM4
Nonframeshift variant in NON repetitive region in NM_021614.4.
BS2
High AC in GnomAdExome4 at 18 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
KCNN2NM_021614.4 linkc.428_439delACGCGCAGCAGT p.Tyr143_Gln146del disruptive_inframe_deletion Exon 1 of 8 ENST00000673685.1 NP_067627.3 Q9H2S1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
KCNN2ENST00000673685.1 linkc.428_439delACGCGCAGCAGT p.Tyr143_Gln146del disruptive_inframe_deletion Exon 1 of 8 NM_021614.4 ENSP00000501239.1 A0A669KBH3
KCNN2ENST00000512097.10 linkc.626_637delACGCGCAGCAGT p.Tyr209_Gln212del disruptive_inframe_deletion Exon 6 of 13 5 ENSP00000427120.4 A0A3F2YNY5

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.0000391
AC:
18
AN:
460938
Hom.:
0
AF XY:
0.0000292
AC XY:
7
AN XY:
239774
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.0000800
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000266
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000228
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33
Bravo
AF:
0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1242600338; hg19: chr5-113698255; API