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NM_020778.5(ALPK3):c.4313C>A (p.Ser1438Ter) AND ALPK3-related disorder

Germline classification:
Pathogenic (1 submission)
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:
RCV003335962.1

Allele description [Variation Report for NM_020778.5(ALPK3):c.4313C>A (p.Ser1438Ter)]

NM_020778.5(ALPK3):c.4313C>A (p.Ser1438Ter)

Gene:
ALPK3:alpha kinase 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
15q25.3
Genomic location:
Preferred name:
NM_020778.5(ALPK3):c.4313C>A (p.Ser1438Ter)
HGVS:
  • NC_000015.10:g.84862818C>A
  • NG_054748.1:g.51188C>A
  • NM_020778.5:c.4313C>AMANE SELECT
  • NP_065829.4:p.Ser1438Ter
  • NC_000015.9:g.85406049C>A
  • NM_020778.4:c.4919C>A
Protein change:
S1438*
Molecular consequence:
  • NM_020778.5:c.4313C>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
ALPK3-related disorder
Synonyms:
ALPK3-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004046377Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenicgermlineclinical 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 Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego, SCV004046377.1

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

Description

This nonsense variant is located within a region of homozygosity on chromosome 15. The variant is found in exon 10 of 14 is predicted to result in loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay (NMD). This variant has not been previously reported or functionally characterized in the literature to our knowledge. However, other loss of function variants downstream of this variant have been reported in affected individuals in the ClinVar database and the Human Gene Mutation Database (HGMD). It is absent from the gnomAD population database and thus is presumed to be rare. Based on the available evidence, the c.4919C>A (p.Ser1640Ter) variant is classified as Pathogenic.

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

Last Updated: May 12, 2024