X-48962751-G-A

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2

The NM_004979.6(KCND1):​c.1774C>T​(p.Arg592Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000422 in 1,208,586 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 18 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000018 ( 0 hom., 1 hem., cov: 22)
Exomes 𝑓: 0.000045 ( 0 hom. 17 hem. )

Consequence

KCND1
NM_004979.6 missense

Scores

2
7
8

Clinical Significance

Uncertain significance criteria provided, single submitter P:1U:1

Conservation

PhyloP100: 1.85
Variant links:
Genes affected
KCND1 (HGNC:6237): (potassium voltage-gated channel subfamily D member 1) This gene encodes a multipass membrane protein that comprises the pore subunit of the voltage-gated A-type potassium channel, which functions in the repolarization of membrane action potentials. Activity of voltage-gated potassium channels is important in a number of physiological processes, among them the regulation of neurotransmitter release, heart rate, insulin secretion, and smooth muscle contraction. [provided by RefSeq, Aug 2013]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.38268203).
BS2
High Hemizygotes in GnomAdExome4 at 17 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
KCND1NM_004979.6 linkc.1774C>T p.Arg592Trp missense_variant 6/6 ENST00000218176.4 NP_004970.3 Q9NSA2-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
KCND1ENST00000218176.4 linkc.1774C>T p.Arg592Trp missense_variant 6/61 NM_004979.6 ENSP00000218176.3 Q9NSA2-1
KCND1ENST00000376477.5 linkc.643C>T p.Arg215Trp missense_variant 5/52 ENSP00000365660.1 Q9NSA2-2

Frequencies

GnomAD3 genomes
AF:
0.0000180
AC:
2
AN:
111258
Hom.:
0
Cov.:
22
AF XY:
0.0000299
AC XY:
1
AN XY:
33418
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000281
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000189
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000447
AC:
49
AN:
1097328
Hom.:
0
Cov.:
30
AF XY:
0.0000469
AC XY:
17
AN XY:
362724
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000558
Gnomad4 OTH exome
AF:
0.0000434
GnomAD4 genome
AF:
0.0000180
AC:
2
AN:
111258
Hom.:
0
Cov.:
22
AF XY:
0.0000299
AC XY:
1
AN XY:
33418
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000281
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000189
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.0000151

ClinVar

Significance: Uncertain significance
Submissions summary: Pathogenic:1Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Short stature Pathogenic:1
Likely pathogenic, no assertion criteria providedcase-controlInstitute of Human Genetics, FAU Erlangen, Friedrich-Alexander-Universität Erlangen-NürnbergNov 18, 2001- -
not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsJul 14, 2021The c.1774C>T (p.R592W) alteration is located in exon 6 (coding exon 6) of the KCND1 gene. This alteration results from a C to T substitution at nucleotide position 1774, causing the arginine (R) at amino acid position 592 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.17
BayesDel_addAF
Uncertain
0.059
T
BayesDel_noAF
Benign
-0.15
CADD
Uncertain
24
DANN
Pathogenic
1.0
DEOGEN2
Benign
0.13
.;T
FATHMM_MKL
Uncertain
0.93
D
LIST_S2
Uncertain
0.92
D;D
M_CAP
Pathogenic
0.74
D
MetaRNN
Benign
0.38
T;T
MetaSVM
Uncertain
0.79
D
MutationAssessor
Benign
0.0
.;N
PrimateAI
Benign
0.41
T
PROVEAN
Benign
-2.0
N;N
REVEL
Uncertain
0.38
Sift
Uncertain
0.0050
D;D
Sift4G
Uncertain
0.025
D;D
Polyphen
0.84
.;P
Vest4
0.21
MVP
1.0
MPC
0.16
ClinPred
0.59
D
GERP RS
4.1
Varity_R
0.17
gMVP
0.53

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

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

Other links and lift over

dbSNP: rs1230432769; hg19: chrX-48820012; API