NM_018249.6(CDK5RAP2):c.5579T>A (p.Leu1860Ter) AND Microcephaly 3, primary, autosomal recessive

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Mar 17, 2024
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:: RCV003988737.3

Allele description [Variation Report for NM_018249.6(CDK5RAP2):c.5579T>A (p.Leu1860Ter)]

NM_018249.6(CDK5RAP2):c.5579T>A (p.Leu1860Ter)

Gene:

CDK5RAP2:CDK5 regulatory subunit associated protein 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q33.2

Genomic location:

Preferred name:

NM_018249.6(CDK5RAP2):c.5579T>A (p.Leu1860Ter)

HGVS:

NC_000009.12:g.120389787A>T
NG_008999.1:g.195373T>A
NM_001011649.3:c.5342T>A
NM_001272039.2:c.4889T>A
NM_001410992.1:c.5480T>A
NM_001410993.1:c.5483T>A
NM_001410994.1:c.5576T>A
NM_018249.6:c.5579T>AMANE SELECT
NP_001011649.1:p.Leu1781Ter
NP_001258968.1:p.Leu1630Ter
NP_001397921.1:p.Leu1827Ter
NP_001397922.1:p.Leu1828Ter
NP_001397923.1:p.Leu1859Ter
NP_060719.4:p.Leu1860Ter
NC_000009.11:g.123152065A>T
NR_073554.2:n.5843T>A
NR_073555.2:n.5766T>A
NR_073556.2:n.5975T>A
NR_073557.2:n.5848T>A
NR_073558.2:n.5845T>A

Protein change:

L1630*

Molecular consequence:

NR_073554.2:n.5843T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_073555.2:n.5766T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_073556.2:n.5975T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_073557.2:n.5848T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_073558.2:n.5845T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001011649.3:c.5342T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001272039.2:c.4889T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001410992.1:c.5480T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001410993.1:c.5483T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001410994.1:c.5576T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_018249.6:c.5579T>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Microcephaly 3, primary, autosomal recessive
Identifiers:: MONDO: MONDO:0011488; MedGen: C1858108; Orphanet: 2512; OMIM: 604804

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004804886	Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Mar 17, 2024)	germline	research	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004804886

Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Mar 17, 2024)

germline

research

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	research

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 Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, SCV004804886.2

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

#	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: Aug 4, 2024

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