rs2229006

Positions:

• chr20-49373713-G-A
• chr20-49373713-G-C
• chr20-49373713-G-T

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PM2 PP2 BP4_Moderate BP6_Moderate

The NM_004975.4(KCNB1):​c.1847C>T​(p.Thr616Ile) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T616N) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: KCNB1 NM_004975.4 missense
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 4.96

Genes affected

KCNB1 (HGNC:6231): (potassium voltage-gated channel subfamily B member 1) Voltage-gated potassium (Kv) 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, shab-related subfamily. This member is a delayed rectifier potassium channel and its activity is modulated by some other family members. [provided by RefSeq, Jul 2008]

ENSG00000290421 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant in gene, where missense usually causes diseases (based on misZ statistic), KCNB1. . Gene score misZ: 4.269 (greater than the threshold 3.09). Trascript score misZ: 5.3923 (greater than threshold 3.09). The gene has 76 curated pathogenic missense variants (we use a threshold of 10). The gene has 110 curated benign missense variants. GenCC has associacion of the gene with undetermined early-onset epileptic encephalopathy, complex neurodevelopmental disorder, developmental and epileptic encephalopathy, 26.
• BP4: Computational evidence support a benign effect (MetaRNN=0.074272424).
• BP6: Variant 20-49373713-G-A is Benign according to our data. Variant chr20-49373713-G-A is described in ClinVar as [Benign]. Clinvar id is 833862.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KCNB1	NM_004975.4	c.1847C>T	p.Thr616Ile	missense_variant	2/2	ENST00000371741.6	NP_004966.1
KCNB1	XM_011528799.3	c.1847C>T	p.Thr616Ile	missense_variant	3/3		XP_011527101.1
LOC105372649	XR_001754659.2	n.1201+41689G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KCNB1	ENST00000371741.6	c.1847C>T	p.Thr616Ile	missense_variant	2/2	1	NM_004975.4	ENSP00000360806.3
KCNB1	ENST00000635465.1	c.1847C>T	p.Thr616Ile	missense_variant	3/3	1		ENSP00000489193.1
KCNB1	ENST00000635878.1	c.97-74330C>T		intron_variant		5		ENSP00000489908.1
ENSG00000290421	ENST00000637341.1	n.206+41689G>A		intron_variant		5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Developmental and epileptic encephalopathy, 26 Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Oct 08, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.096
BayesDel_addAF	Benign	-0.37	T
BayesDel_noAF	Benign	-0.76
CADD	Benign	19
DANN	Benign	0.67
DEOGEN2	Benign	0.26	T;T
Eigen	Benign	-0.57
Eigen_PC	Benign	-0.44
FATHMM_MKL	Benign	0.16	N
LIST_S2	Benign	0.63	.;T
M_CAP	Benign	0.0032	T
MetaRNN	Benign	0.074	T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	-0.55	N;N
PrimateAI	Benign	0.47	T
PROVEAN	Benign	-0.82	N;.
REVEL	Benign	0.11
Sift	Benign	0.46	T;.
Sift4G	Benign	0.20	T;T
Polyphen		0.0	B;B
Vest4		0.021
MutPred		0.40		Loss of phosphorylation at T616 (P = 0.0319);Loss of phosphorylation at T616 (P = 0.0319);
MVP		0.25
MPC		0.20
ClinPred		0.47	T
GERP RS		5.0
Varity_R		0.074
gMVP		0.21

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

LitVar

Other links and lift over

dbSNP: rs2229006; hg19: chr20-47990250;