NM_001378969.1(KCND3):c.1174G>A (p.Val392Ile) AND not provided

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: Feb 13, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000444260.5

Allele description [Variation Report for NM_001378969.1(KCND3):c.1174G>A (p.Val392Ile)]

NM_001378969.1(KCND3):c.1174G>A (p.Val392Ile)

Gene:

KCND3:potassium voltage-gated channel subfamily D member 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p13.2

Genomic location:

Preferred name:

NM_001378969.1(KCND3):c.1174G>A (p.Val392Ile)

HGVS:

NC_000001.11:g.111787039C>T
NG_032011.2:g.207117G>A
NM_001378969.1:c.1174G>AMANE SELECT
NM_001378970.1:c.1174G>A
NM_004980.5:c.1174G>A
NM_172198.3:c.1174G>A
NP_001365898.1:p.Val392Ile
NP_001365899.1:p.Val392Ile
NP_004971.2:p.Val392Ile
NP_004971.2:p.Val392Ile
NP_751948.1:p.Val392Ile
LRG_445t1:c.1174G>A
LRG_445:g.207117G>A
LRG_445p1:p.Val392Ile
NC_000001.10:g.112329661C>T
NM_004980.4:c.1174G>A
Q9UK17:p.Val392Ile

Protein change:

V392I; VAL392ILE

Links:

UniProtKB: Q9UK17#VAR_067694; OMIM: 605411.0007; dbSNP: rs786205867

NCBI 1000 Genomes Browser:

rs786205867

Molecular consequence:

NM_001378969.1:c.1174G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001378970.1:c.1174G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004980.5:c.1174G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_172198.3:c.1174G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000521303	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Feb 13, 2024)	germline	clinical testing	Citation Link,
SCV005198519	Clinical Genetics Laboratory, Skane University Hospital Lund	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (May 8, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000521303

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Feb 13, 2024)

germline

clinical testing

Citation Link,

SCV005198519

Clinical Genetics Laboratory, Skane University Hospital Lund

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(May 8, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From GeneDx, SCV000521303.6

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Previously reported in a 20-year-old male with SUD and a history of two syncopal episodes; however, no premortem ECG was available and familial segregation studies were declined (PMID: 22457051); Published functional studies demonstrated p.(V392I) significantly increased peak current density compared to wild type and slowed recovery from inactivation, suggestive of a mixed electrophysiological phenotype (PMID: 22457051); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 23400760, 34426522, 34361012, 30662450, 32921676, 32901917, 30776697, 34709746, Ahammed2023[Review], 36376730, 33920294, 35861988, 35388935, 35813061, 22457051)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Clinical Genetics Laboratory, Skane University Hospital Lund, SCV005198519.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 8, 2024

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