NM_003718.5(CDK13):c.2609A>G (p.Tyr870Cys) AND Congenital heart defects, dysmorphic facial features, and intellectual developmental disorder

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jun 8, 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:: RCV002254894.2

Allele description [Variation Report for NM_003718.5(CDK13):c.2609A>G (p.Tyr870Cys)]

NM_003718.5(CDK13):c.2609A>G (p.Tyr870Cys)

Gene:

CDK13:cyclin dependent kinase 13 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7p14.1

Genomic location:

Preferred name:

NM_003718.5(CDK13):c.2609A>G (p.Tyr870Cys)

HGVS:

NC_000007.14:g.40062834A>G
NG_052965.1:g.117475A>G
NM_003718.5:c.2609A>GMANE SELECT
NM_031267.3:c.2609A>G
NP_003709.3:p.Tyr870Cys
NP_112557.2:p.Tyr870Cys
NC_000007.13:g.40102433A>G

Protein change:

Y870C

Links:

dbSNP: rs2150526766

NCBI 1000 Genomes Browser:

rs2150526766

Molecular consequence:

NM_003718.5:c.2609A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_031267.3:c.2609A>G - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: Congenital heart defects, dysmorphic facial features, and intellectual developmental disorder (CHDFIDD)
Identifiers:: MONDO: MONDO:0044302; MedGen: C4479246; OMIM: 617360

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002526128	Institute of Human Genetics, University Hospital Muenster	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jun 8, 2022)	de novo	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

SCV002526128

Institute of Human Genetics, University Hospital Muenster

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Jun 8, 2022)

de novo

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	de novo	yes	1	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 Institute of Human Genetics, University Hospital Muenster, SCV002526128.1

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

Description

ACMG categories: PS2,PM1,PM2,PP3,BP1

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

Last Updated: Jul 15, 2024

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