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NM_000397.4(CYBB):c.141+1del AND Granulomatous disease, chronic, X-linked

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 22, 2019
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:
RCV001246396.6

Allele description [Variation Report for NM_000397.4(CYBB):c.141+1del]

NM_000397.4(CYBB):c.141+1del

Gene:
CYBB:cytochrome b-245 beta chain [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
Xp21.1
Genomic location:
Preferred name:
NM_000397.4(CYBB):c.141+1del
HGVS:
  • NC_000023.11:g.37782184del
  • NG_009065.1:g.7168del
  • NM_000397.4:c.141+1delMANE SELECT
  • LRG_53t1:c.141del
  • LRG_53:g.7168del
  • NC_000023.10:g.37641434del
  • NC_000023.10:g.37641437del
  • NM_000397.3:c.141del
Links:
dbSNP: rs1928965951
NCBI 1000 Genomes Browser:
rs1928965951
Molecular consequence:
  • NM_000397.4:c.141+1del - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
Granulomatous disease, chronic, X-linked
Synonyms:
CYTOCHROME b-NEGATIVE GRANULOMATOUS DISEASE, CHRONIC, X-LINKED; GRANULOMATOUS DISEASE, CHRONIC, X-LINKED, SOMATIC MOSAIC
Identifiers:
MONDO: MONDO:0010600; MedGen: C1844376; Orphanet: 379; OMIM: 306400

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001419746Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Sep 22, 2019) 		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

X-Linked chronic granulomatous disease: mutations in the CYBB gene encoding the gp91-phox component of respiratory-burst oxidase.

Rae J, Newburger PE, Dinauer MC, Noack D, Hopkins PJ, Kuruto R, Curnutte JT.

Am J Hum Genet. 1998 Jun;62(6):1320-31.

PubMed [citation]
PMID:
9585602
PMCID:
PMC1377153

Hematologically important mutations: X-linked chronic granulomatous disease (third update).

Roos D, Kuhns DB, Maddalena A, Roesler J, Lopez JA, Ariga T, Avcin T, de Boer M, Bustamante J, Condino-Neto A, Di Matteo G, He J, Hill HR, Holland SM, Kannengiesser C, Köker MY, Kondratenko I, van Leeuwen K, Malech HL, Marodi L, Nunoi H, Stasia MJ, et al.

Blood Cells Mol Dis. 2010 Oct 15;45(3):246-65. doi: 10.1016/j.bcmd.2010.07.012. Epub 2010 Aug 21. Review.

PubMed [citation]
PMID:
20729109
PMCID:
PMC4360070
See all PubMed Citations (4)

Details of each submission

From Invitae, SCV001419746.4

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

Description

For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in CYBB are known to be pathogenic (PMID: 9585602, 20729109). This variant has been observed in an individual affected with clinical features of chronic granulomatous disease (PMID: 8634410). This variant may also be known as c.151del, c.152del, c.153del, or c.153+1del in the literature. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Ser48Glnfs*13) in the CYBB gene. It is expected to result in an absent or disrupted protein product.

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

Last Updated: Feb 20, 2024