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NM_001378969.1(KCND3):c.911C>T (p.Ser304Phe) AND Spinocerebellar ataxia type 19/22

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Sep 2, 2022
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:
RCV002273254.3

Allele description [Variation Report for NM_001378969.1(KCND3):c.911C>T (p.Ser304Phe)]

NM_001378969.1(KCND3):c.911C>T (p.Ser304Phe)

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.911C>T (p.Ser304Phe)
HGVS:
  • NC_000001.11:g.111981816G>A
  • NG_032011.2:g.12340C>T
  • NM_001378969.1:c.911C>TMANE SELECT
  • NM_001378970.1:c.911C>T
  • NM_004980.5:c.911C>T
  • NM_172198.3:c.911C>T
  • NP_001365898.1:p.Ser304Phe
  • NP_001365899.1:p.Ser304Phe
  • NP_004971.2:p.Ser304Phe
  • NP_751948.1:p.Ser304Phe
  • LRG_445t1:c.911C>T
  • LRG_445:g.12340C>T
  • NC_000001.10:g.112524438G>A
  • NM_004980.4:c.911C>T
Protein change:
S304F
Links:
dbSNP: rs2101995530
NCBI 1000 Genomes Browser:
rs2101995530
Molecular consequence:
  • NM_001378969.1:c.911C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001378970.1:c.911C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004980.5:c.911C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_172198.3:c.911C>T - 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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002558016Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Sep 2, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical 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 Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002558016.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

A heterozygous missense variant was identified, NM_004980.4(KCND3):c.911C>T in exon 2 of 8 of the KCND3 gene. This substitution is predicted to create a major amino acid change from serine to phenylalanine at position 304 of the protein, NP_004971.2(KCND3):p.(Ser304Phe). The serine at this position has very high conservation (100 vertebrates, UCSC), and is located within the ion transporter functional domain. In silico software predicts this variant to be disease causing (Polyphen, SIFT, CADD, Mutation Taster). The variant is not present in the gnomAD population database. The variant has not been previously reported in a clinical testing setting. A different variant in the same codon resulting in a change to proline has been reported but with no classification (LOVD). Subsequent analysis of parental samples indicated that this variant is de novo. Based on information available at the time of curation, this variant has been reclassified as LIKELY PATHOGENIC.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 16, 2025