NM_015076.5(CDK19):c.95A>G (p.Tyr32Cys) AND Developmental and epileptic encephalopathy, 87

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (2 submissions)
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:: RCV001252680.12

Allele description

NM_015076.5(CDK19):c.95A>G (p.Tyr32Cys)

Genes:

AMD1:adenosylmethionine decarboxylase 1 [Gene - OMIM - HGNC]
CDK19:cyclin dependent kinase 19 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

6q21

Genomic location:

Preferred name:

NM_015076.5(CDK19):c.95A>G (p.Tyr32Cys)

HGVS:

NC_000006.12:g.110815042T>C
NG_109014.1:g.579T>C
NM_001287215.2:c.-98+227T>C
NM_001300960.2:c.95A>G
NM_001300963.2:c.-115+529A>G
NM_001300964.2:c.-53+766A>G
NM_015076.5:c.95A>GMANE SELECT
NP_001287889.1:p.Tyr32Cys
NP_055891.1:p.Tyr32Cys
NC_000006.11:g.111136245T>C

Protein change:

Y32C

Links:

dbSNP: rs1783517622

NCBI 1000 Genomes Browser:

rs1783517622

Molecular consequence:

NM_001287215.2:c.-98+227T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001300963.2:c.-115+529A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001300964.2:c.-53+766A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001300960.2:c.95A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_015076.5:c.95A>G - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: Developmental and epileptic encephalopathy, 87
Synonyms:: EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 87
Identifiers:: MONDO: MONDO:0030059; MedGen: C5394501; OMIM: 618916

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001428439	Zarate Arkansas Children's Genetics Clinic, Arkansas Children's Hospital	no assertion criteria provided	Likely pathogenic (Aug 11, 2020)	de novo	clinical testing
SCV004047804	Neuberg Centre For Genomic Medicine, NCGM	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance	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

SCV001428439

Zarate Arkansas Children's Genetics Clinic, Arkansas Children's Hospital

no assertion criteria provided

Likely pathogenic
(Aug 11, 2020)

de novo

clinical testing

SCV004047804

Neuberg Centre For Genomic Medicine, NCGM

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance

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
not provided	de novo	yes	1	not provided	not provided	1	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 Zarate Arkansas Children's Genetics Clinic, Arkansas Children's Hospital, SCV001428439.1

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

Description

De novo variant, in conserved residue, absent in population databases, located in functional domain with other variants, anoter substitution at residue interpreted as pathogenic

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

From Neuberg Centre For Genomic Medicine, NCGM, SCV004047804.1

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

Description

The c.95A>G(p.Tyr32Cys) missense variant in CDK19 gene has been submitted to ClinVar as Likely Pathogenic, but no details are available for independent assessment. It has not been reported in affected individuals. The p.Tyr32Cys variant is novel (not in any individuals) in gnomAD Exomes and 1000 Genomes. The amino acid Tyr at position 32 is changed to a Cys changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as Variant of Uncertain Significance (VUS).

#	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: Apr 20, 2024

ClinVar

Relating variation to medicine