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NM_000265.7(NCF1):c.579G>A (p.Trp193Ter) AND Chronic granulomatous disease

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 9, 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:
RCV002298619.2

Allele description [Variation Report for NM_000265.7(NCF1):c.579G>A (p.Trp193Ter)]

NM_000265.7(NCF1):c.579G>A (p.Trp193Ter)

Genes:
LOC106029312:Williams-Beuren syndrome medial block B recombination region [Gene]
NCF1:neutrophil cytosolic factor 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7q11.23
Genomic location:
Preferred name:
NM_000265.7(NCF1):c.579G>A (p.Trp193Ter)
HGVS:
  • NC_000007.14:g.74783529G>A
  • NG_009078.2:g.14566G>A
  • NG_042249.1:g.49693G>A
  • NM_000265.7:c.579G>AMANE SELECT
  • NP_000256.4:p.Trp193Ter
  • LRG_87t1:c.579G>A
  • LRG_87:g.14566G>A
  • LRG_87p1:p.Trp193Ter
  • NC_000007.13:g.74197872G>A
  • NM_000265.4:c.579G>A
  • NM_000265.5:c.579G>A
  • NM_000265.6:c.579G>A
Protein change:
W193*
Links:
dbSNP: rs145360423
NCBI 1000 Genomes Browser:
rs145360423
Molecular consequence:
  • NM_000265.7:c.579G>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Chronic granulomatous disease
Identifiers:
MONDO: MONDO:0018305; MedGen: C0018203; OMIM: PS306400

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002598599Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Pathogenic
(Sep 9, 2022) 		germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Clinical and molecular findings of chronic granulomatous disease in Oman: family studies.

Al-Zadjali S, Al-Tamemi S, Elnour I, AlKindi S, Lapoumeroulie C, Al-Maamari S, Pathare A, Dennison D, Krishnamoorthy R.

Clin Genet. 2015 Feb;87(2):185-9. doi: 10.1111/cge.12351. Epub 2014 Feb 17.

PubMed [citation]
PMID:
24446915

Second Report of Chronic Granulomatous Disease in Jordan: Clinical and Genetic Description of 31 Patients From 21 Different Families, Including Families From Lybia and Iraq.

Bakri FG, Mollin M, Beaumel S, Vigne B, Roux-Buisson N, Al-Wahadneh AM, Alzyoud RM, Hayajneh WA, Daoud AK, Shukair MEA, Karadshe MF, Sarhan MM, Al-Ramahi JAW, Fauré J, Rendu J, Stasia MJ.

Front Immunol. 2021;12:639226. doi: 10.3389/fimmu.2021.639226.

PubMed [citation]
PMID:
33746979
PMCID:
PMC7973097

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV002598599.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

Variant summary: NCF1 c.579G>A (p.Trp193X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic in ClinVar. The variant allele was found at a frequency of 0.00069 in 250032 control chromosomes (gnomAD). This frequency is not higher than predicted for a pathogenic variant in NCF1 causing Chronic Granulomatous Disease (0.00069 vs 0.0011). c.579G>A has been reported in the literature in multiple individuals affected with Chronic Granulomatous Disease and the variant segregated with disease. These data indicate that the variant is very likely to be associated with disease. Eight submitters have provided clinical-significance assessments for this variant to ClinVar after 2014 and all classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

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

Last Updated: Nov 24, 2024