chr5-114362470-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_021614.4(KCNN2):c.331T>G(p.Ser111Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 8/10 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_021614.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KCNN2 | NM_021614.4 | c.331T>G | p.Ser111Ala | missense_variant | 1/8 | ENST00000673685.1 | NP_067627.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KCNN2 | ENST00000673685.1 | c.331T>G | p.Ser111Ala | missense_variant | 1/8 | NM_021614.4 | ENSP00000501239 | P2 | ||
KCNN2 | ENST00000512097.10 | c.529T>G | p.Ser177Ala | missense_variant | 6/13 | 5 | ENSP00000427120 | A2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 3
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Neurodevelopmental disorder with or without variable movement or behavioral abnormalities Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Neuberg Centre For Genomic Medicine, NCGM | - | The missense c.331T>G(p.Ser111Ala) variant in KCNN2 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This variant is absent in gnomAD Exomes and 1000 Genomes. The amino acid Ser at position 111 is changed to a Ala changing protein sequence and it might alter its composition and physico-chemical properties. The amino acid change p.Ser111Ala in KCNN2 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The variant is predicted as damaging by SIFT. For these reasons, this variant has been classified as Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.