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NM_000397.4(CYBB):c.45+6T>C AND Granulomatous disease, chronic, X-linked

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Mar 8, 2023
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:
RCV000011686.8

Allele description [Variation Report for NM_000397.4(CYBB):c.45+6T>C]

NM_000397.4(CYBB):c.45+6T>C

Genes:
LOC130068093:ATAC-STARR-seq lymphoblastoid active region 29519 [Gene]
CYBB:cytochrome b-245 beta chain [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xp21.1
Genomic location:
Preferred name:
NM_000397.4(CYBB):c.45+6T>C
HGVS:
  • NC_000023.11:g.37780128T>C
  • NG_009065.1:g.5112T>C
  • NM_000397.4:c.45+6T>CMANE SELECT
  • LRG_53t1:c.45+6T>C
  • LRG_53:g.5112T>C
  • NC_000023.10:g.37639381T>C
  • NC_000023.10:g.37639381T>C
  • NM_000397.3:c.45+6T>C
Note:
ClinGen staff contributed the HGVS expression for this variant.
Nucleotide change:
IVS1, T-C, +6
Links:
OMIM: 300481.0020; dbSNP: rs1569478551
NCBI 1000 Genomes Browser:
rs1569478551
Molecular consequence:
  • NM_000397.4:c.45+6T>C - intron variant - [Sequence Ontology: SO:0001627]

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

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000031918OMIM
no assertion criteria provided
Pathogenic
(Jun 1, 2000)
germlineliterature only

PubMed (3)
[See all records that cite these PMIDs]

SCV004298946Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Mar 8, 2023)
germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Partial correction of the phagocyte defect in patients with X-linked chronic granulomatous disease by subcutaneous interferon gamma.

Ezekowitz RA, Dinauer MC, Jaffe HS, Orkin SH, Newburger PE.

N Engl J Med. 1988 Jul 21;319(3):146-51.

PubMed [citation]
PMID:
2838754

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

Buratti E, Chivers M, Královicová J, Romano M, Baralle M, Krainer AR, Vorechovsky I.

Nucleic Acids Res. 2007;35(13):4250-63. Epub 2007 Jun 18.

PubMed [citation]
PMID:
17576681
PMCID:
PMC1934990
See all PubMed Citations (6)

Details of each submission

From OMIM, SCV000031918.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (3)

Description

In a patient with X-linked CGD (306400) first reported by Ezekowitz et al. (1988), Rae et al. (1998) identified a T-to-C change in the 5-prime splice site of intron 1 of the CYBB gene, resulting in a diminished level of p91-phox. In this patient, Ezekowitz et al. (1988) found that interferon-gamma (IFNG; 147570), an activator of phagocytes, resulted in a 5- to 10-fold increase in superoxide production by granulocytes and monocytes, a proportionate rise in granulocyte bactericidal activity, and an increase in the cellular contents of phagocyte cytochrome b and immunoreactive cytochrome b heavy chain. In other CGD group studies, however, no apparent increases in phagocyte superoxide generation were observed. For that reason, the patient studied by Ezekowitz et al. (1988) was considered to be an exceptional case. Condino-Neto and Newburger (2000) proposed that IFN-gamma improved the splicing efficiency of CYBB gene transcripts in that patient and corrected a nuclear processing defect due to the intronic mutation by augmenting nuclear export of normal transcripts.

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

From Invitae, SCV004298946.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

For these reasons, this variant has been classified as Pathogenic. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant is associated with altered splicing resulting in some transcripts that retain intron 1 (PMID: 10828042). Studies have shown that this variant alters CYBB gene expression (PMID: 10828042). ClinVar contains an entry for this variant (Variation ID: 10939). This variant has been observed in individuals with chronic granulomatous disease (PMID: 9585602; Invitae). This variant is not present in population databases (gnomAD no frequency). This sequence change falls in intron 1 of the CYBB gene. It does not directly change the encoded amino acid sequence of the CYBB protein. It affects a nucleotide within the consensus splice site.

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

Last Updated: Feb 20, 2024