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NC_000013.10:g.(?_24293859)_(26594123_?)del AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jun 29, 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:
RCV003119915.5

Allele description [Variation Report for NC_000013.10:g.(?_24293859)_(26594123_?)del]

NC_000013.10:g.(?_24293859)_(26594123_?)del

Genes:
  • AMER2:APC membrane recruitment protein 2 [Gene - OMIM - HGNC]
  • ATP12A:ATPase H+/K+ transporting non-gastric alpha2 subunit [Gene - OMIM - HGNC]
  • ATP8A2:ATPase phospholipid transporting 8A2 [Gene - OMIM - HGNC]
  • C1QTNF9:C1q and TNF related 9 [Gene - OMIM - HGNC]
  • C1QTNF9B:C1q and TNF related 9B [Gene - OMIM - HGNC]
  • CENPJ:centromere protein J [Gene - OMIM - HGNC]
  • MIPEP:mitochondrial intermediate peptidase [Gene - OMIM - HGNC]
  • MTMR6:myotubularin related protein 6 [Gene - OMIM - HGNC]
  • NUP58:nucleoporin 58 [Gene - OMIM - HGNC]
  • PABPC3:poly(A) binding protein cytoplasmic 3 [Gene - OMIM - HGNC]
  • PARP4:poly(ADP-ribose) polymerase family member 4 [Gene - OMIM - HGNC]
  • PCOTH:prostate and testis expressed opposite C1QTNF9B and MIPEP [Gene - OMIM - HGNC]
  • RNF17:ring finger protein 17 [Gene - OMIM - HGNC]
  • SPATA13:spermatogenesis associated 13 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
13q12.12-12.13
Genomic location:
Chr13: 24293859 - 26594123 (on Assembly GRCh37)
Preferred name:
NC_000013.10:g.(?_24293859)_(26594123_?)del
HGVS:
NC_000013.10:g.(?_24293859)_(26594123_?)del

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003795179Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jun 29, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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, SCV003795179.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with CENPJ-related conditions. A gross deletion of the genomic region encompassing the full coding sequence of the CENPJ gene has been identified. Loss-of-function variants in CENPJ are known to be pathogenic (PMID: 15793586, 16900296, 20522431). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes.

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

Last Updated: Sep 29, 2024