NM_001378969.1(KCND3):c.514G>A (p.Ala172Thr) AND Spinocerebellar ataxia type 19/22

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 25, 2021
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV001868114.4

Allele description [Variation Report for NM_001378969.1(KCND3):c.514G>A (p.Ala172Thr)]

NM_001378969.1(KCND3):c.514G>A (p.Ala172Thr)

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.514G>A (p.Ala172Thr)

HGVS:

NC_000001.11:g.111982213C>T
NG_032011.2:g.11943G>A
NM_001378969.1:c.514G>AMANE SELECT
NM_001378970.1:c.514G>A
NM_004980.5:c.514G>A
NM_172198.3:c.514G>A
NP_001365898.1:p.Ala172Thr
NP_001365899.1:p.Ala172Thr
NP_004971.2:p.Ala172Thr
NP_004971.2:p.Ala172Thr
NP_751948.1:p.Ala172Thr
LRG_445t1:c.514G>A
LRG_445:g.11943G>A
LRG_445p1:p.Ala172Thr
NC_000001.10:g.112524835C>T
NM_004980.4:c.514G>A

Protein change:

A172T

Links:

dbSNP: rs149488365

NCBI 1000 Genomes Browser:

rs149488365

Molecular consequence:

NM_001378969.1:c.514G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001378970.1:c.514G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004980.5:c.514G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_172198.3:c.514G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Spinocerebellar ataxia type 19/22 (SCA19)
Synonyms:: Spinocerebellar ataxia 19; Spinocerebellar ataxia 22
Identifiers:: MONDO: MONDO:0011819; MedGen: C1846367; Orphanet: 98772; OMIM: 607346

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BioProject Links for Nucleotide (Select 312227302) (1)
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dbVar
Heterospilus sp. BOLD:AAI1747 voucher Cham-0205 cytochrome oxidase subunit 1 (CO...
Heterospilus sp. BOLD:AAI1747 voucher Cham-0205 cytochrome oxidase subunit 1 (COI) gene, partial cds; mitochondrial
gi|301084899|gnl|uoguelph|ASDOR301- I-5P|gb|HM434464.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002186234	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 25, 2021)	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

SCV002186234

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 25, 2021)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002186234.3

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C55"). ClinVar contains an entry for this variant (Variation ID: 519447). This variant has not been reported in the literature in individuals affected with KCND3-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces alanine with threonine at codon 172 of the KCND3 protein (p.Ala172Thr). The alanine residue is highly conserved and there is a small physicochemical difference between alanine and threonine.

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

Last Updated: Sep 29, 2024

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