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NC_000023.10:g.(?_117629935)_(119761021_?)del AND X-linked intellectual disability Cabezas type

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jul 23, 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:
RCV003113287.4

Allele description [Variation Report for NC_000023.10:g.(?_117629935)_(119761021_?)del]

NC_000023.10:g.(?_117629935)_(119761021_?)del

Genes:
  • AKAP14:A-kinase anchoring protein 14 [Gene - OMIM - HGNC]
  • ATP1B4:ATPase Na+/K+ transporting family member beta 4 [Gene - OMIM - HGNC]
  • C1GALT1C1:C1GALT1 specific chaperone 1 [Gene - OMIM - HGNC]
  • KIAA1210:KIAA1210 [Gene - OMIM - HGNC]
  • LONRF3:LON peptidase N-terminal domain and ring finger 3 [Gene - HGNC]
  • MCTS1:MCTS1 re-initiation and release factor [Gene - OMIM - HGNC]
  • NDUFA1:NADH:ubiquinone oxidoreductase subunit A1 [Gene - OMIM - HGNC]
  • NKAP:NFKB activating protein [Gene - OMIM - HGNC]
  • NKRF:NFKB repressing factor [Gene - OMIM - HGNC]
  • RHOXF1:Rhox homeobox family member 1 [Gene - OMIM - HGNC]
  • RHOXF2:Rhox homeobox family member 2 [Gene - OMIM - HGNC]
  • RHOXF2B:Rhox homeobox family member 2B [Gene - HGNC]
  • STEEP1:STING1 ER exit protein 1 [Gene - OMIM - HGNC]
  • UPF3B:UPF3B regulator of nonsense mediated mRNA decay [Gene - OMIM - HGNC]
  • CUL4B:cullin 4B [Gene - OMIM - HGNC]
  • DOCK11:dedicator of cytokinesis 11 [Gene - OMIM - HGNC]
  • IL13RA1:interleukin 13 receptor subunit alpha 1 [Gene - OMIM - HGNC]
  • LAMP2:lysosomal associated membrane protein 2 [Gene - OMIM - HGNC]
  • PGRMC1:progesterone receptor membrane component 1 [Gene - OMIM - HGNC]
  • RPL39:ribosomal protein L39 [Gene - OMIM - HGNC]
  • RNF113A:ring finger protein 113A [Gene - OMIM - HGNC]
  • SEPTIN6:septin 6 [Gene - OMIM - HGNC]
  • SLC25A43:solute carrier family 25 member 43 [Gene - OMIM - HGNC]
  • SLC25A5:solute carrier family 25 member 5 [Gene - OMIM - HGNC]
  • SOWAHD:sosondowah ankyrin repeat domain family member D [Gene - HGNC]
  • TMEM255A:transmembrane protein 255A [Gene - HGNC]
  • UBE2A:ubiquitin conjugating enzyme E2 A [Gene - OMIM - HGNC]
  • ZCCHC12:zinc finger CCHC-type containing 12 [Gene - OMIM - HGNC]
  • ZBTB33:zinc finger and BTB domain containing 33 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
Xq24
Genomic location:
ChrX: 117629935 - 119761021 (on Assembly GRCh37)
Preferred name:
NC_000023.10:g.(?_117629935)_(119761021_?)del
HGVS:
NC_000023.10:g.(?_117629935)_(119761021_?)del

Condition(s)

Name:
X-linked intellectual disability Cabezas type (MRXSC)
Synonyms:
CABEZAS SYNDROME; MENTAL RETARDATION, X-LINKED, SYNDROMIC 15; Mental retardation with short stature, hypogonadism and abnormal gait, X-linked; See all synonyms [MedGen]
Identifiers:
Gene: 114890; MONDO: MONDO:0010306; MedGen: C1845861; Orphanet: 85289; Orphanet: 85293; OMIM: 300354

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003791373Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jul 23, 2022) 		germlineclinical testing

PubMed (3)
[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

Mutations in CUL4B, which encodes a ubiquitin E3 ligase subunit, cause an X-linked mental retardation syndrome associated with aggressive outbursts, seizures, relative macrocephaly, central obesity, hypogonadism, pes cavus, and tremor.

Tarpey PS, Raymond FL, O'Meara S, Edkins S, Teague J, Butler A, Dicks E, Stevens C, Tofts C, Avis T, Barthorpe S, Buck G, Cole J, Gray K, Halliday K, Harrison R, Hills K, Jenkinson A, Jones D, Menzies A, Mironenko T, Perry J, et al.

Am J Hum Genet. 2007 Feb;80(2):345-52. Epub 2007 Jan 4.

PubMed [citation]
PMID:
17236139
PMCID:
PMC1785336

Variants in CUL4B are associated with cerebral malformations.

Vulto-van Silfhout AT, Nakagawa T, Bahi-Buisson N, Haas SA, Hu H, Bienek M, Vissers LE, Gilissen C, Tzschach A, Busche A, Müsebeck J, Rump P, Mathijssen IB, Avela K, Somer M, Doagu F, Philips AK, Rauch A, Baumer A, Voesenek K, Poirier K, Vigneron J, et al.

Hum Mutat. 2015 Jan;36(1):106-17. doi: 10.1002/humu.22718.

PubMed [citation]
PMID:
25385192
PMCID:
PMC4608231
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003791373.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

A gross deletion of the genomic region encompassing the full coding sequence of the CUL4B gene has been identified. Loss-of-function variants in CUL4B are known to be pathogenic (PMID: 17236139, 25385192). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. This variant has not been reported in the literature in individuals affected with CUL4B-related conditions. For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Sep 29, 2024