NM_018451.5(CENPJ):c.1434del (p.Lys479fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 21, 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:: RCV003770857.2

Allele description [Variation Report for NM_018451.5(CENPJ):c.1434del (p.Lys479fs)]

NM_018451.5(CENPJ):c.1434del (p.Lys479fs)

Gene:

CENPJ:centromere protein J [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

13q12.13

Genomic location:

Preferred name:

NM_018451.5(CENPJ):c.1434del (p.Lys479fs)

HGVS:

NC_000013.11:g.24906607del
NG_009165.2:g.21344del
NM_018451.5:c.1434delMANE SELECT
NP_060921.3:p.Lys479fs
NC_000013.10:g.25480742del
NC_000013.10:g.25480745del
NM_018451.4:c.1434delG
NR_047594.2:n.1601del
NR_047595.2:n.1601del

Protein change:

K479fs

Links:

dbSNP: rs1954548327

NCBI 1000 Genomes Browser:

rs1954548327

Molecular consequence:

NM_018451.5:c.1434del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_047594.2:n.1601del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_047595.2:n.1601del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004696558	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 21, 2022)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 15793586, 16900296, 20522431, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004696558

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 21, 2022)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

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	clinical testing

Citations

PubMed

A centrosomal mechanism involving CDK5RAP2 and CENPJ controls brain size.

Bond J, Roberts E, Springell K, Lizarraga SB, Scott S, Higgins J, Hampshire DJ, Morrison EE, Leal GF, Silva EO, Costa SM, Baralle D, Raponi M, Karbani G, Rashid Y, Jafri H, Bennett C, Corry P, Walsh CA, Woods CG.

Nat Genet. 2005 Apr;37(4):353-5. Epub 2005 Mar 27. Erratum in: Nat Genet. 2005 May;37(5):555. Lizarraga, Sophia [corrected to Lizarraga, Sofia B].

PubMed [citation]

PMID:: 15793586

A novel deletion mutation in CENPJ gene in a Pakistani family with autosomal recessive primary microcephaly.

Gul A, Hassan MJ, Hussain S, Raza SI, Chishti MS, Ahmad W.

J Hum Genet. 2006;51(9):760-764. doi: 10.1007/s10038-006-0017-1. Epub 2006 Aug 10.

PubMed [citation]

PMID:: 16900296

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004696558.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 1032801). This variant has not been reported in the literature in individuals affected with CENPJ-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Lys479Argfs*25) in the CENPJ gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CENPJ are known to be pathogenic (PMID: 15793586, 16900296, 20522431).

#	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: Sep 29, 2024

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