NM_000433.3(NCF2):c.55_63del (p.Lys19_Asp21del) AND Chronic granulomatous disease, autosomal recessive cytochrome b-positive, type 2

Clinical significance:Likely pathogenic (Last evaluated: Oct 20, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000002333.5

Allele description [Variation Report for NM_000433.3(NCF2):c.55_63del (p.Lys19_Asp21del)]

NM_000433.3(NCF2):c.55_63del (p.Lys19_Asp21del)

Gene:
NCF2:neutrophil cytosolic factor 2 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
1q25.3
Genomic location:
Preferred name:
NM_000433.3(NCF2):c.55_63del (p.Lys19_Asp21del)
HGVS:
  • NC_000001.11:g.183590271_183590279del
  • NG_007267.1:g.5307_5315del
  • NM_000433.3:c.55_63del
  • NM_001127651.3:c.55_63del
  • NM_001190789.1:c.55_63del
  • NM_001190794.1:c.55_63del
  • NP_000424.2:p.Lys19_Asp21del
  • NP_001121123.1:p.Lys19_Asp21del
  • NP_001177718.1:p.Lys19_Asp21del
  • NP_001177723.1:p.Lys19_Asp21del
  • LRG_88t1:c.55_63del
  • LRG_88:g.5307_5315del
  • LRG_88p1:p.Lys19_Asp21del
  • NC_000001.10:g.183559406_183559414del
  • NM_000433.3:c.55_63delAAGAAGGAC
Links:
OMIM: 608515.0006; dbSNP: rs796065033
NCBI 1000 Genomes Browser:
rs796065033
Molecular consequence:
  • NM_000433.3:c.55_63del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001127651.3:c.55_63del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001190789.1:c.55_63del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001190794.1:c.55_63del - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Name:
Chronic granulomatous disease, autosomal recessive cytochrome b-positive, type 2 (CGD2)
Synonyms:
CGD, AUTOSOMAL RECESSIVE CYTOCHROME b-POSITIVE, TYPE II; GRANULOMATOUS DISEASE, CHRONIC, DUE TO NCF2 DEFICIENCY; GRANULOMATOUS DISEASE, CHRONIC, AUTOSOMAL RECESSIVE, 2; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0009310; MedGen: C1856245; Orphanet: 379; OMIM: 233710

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000022491OMIMno assertion criteria providedPathogenic
(Oct 1, 1999)
germlineliterature only

PubMed (1)
[See all records that cite this PMID]

SCV000956351Invitaecriteria provided, single submitter
Likely pathogenic
(Oct 20, 2018)
germlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

Autosomal recessive chronic granulomatous disease caused by novel mutations in NCF-2, the gene encoding the p67-phox component of phagocyte NADPH oxidase.

Noack D, Rae J, Cross AR, Muñoz J, Salmen S, Mendoza JA, Rossi N, Curnutte JT, Heyworth PG.

Hum Genet. 1999 Nov;105(5):460-7.

PubMed [citation]
PMID:
10598813

Molecular characterization of autosomal recessive chronic granulomatous disease caused by a defect of the nicotinamide adenine dinucleotide phosphate (reduced form) oxidase component p67-phox.

Patiño PJ, Rae J, Noack D, Erickson R, Ding J, de Olarte DG, Curnutte JT.

Blood. 1999 Oct 1;94(7):2505-14.

PubMed [citation]
PMID:
10498624
See all PubMed Citations (4)

Details of each submission

From OMIM, SCV000022491.3

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

Description

In a 16-year-old girl with chronic granulomatous disease (CGD2; 233710), the offspring of unrelated parents who were natives of Mexico, Patino et al. (1999) found compound heterozygosity for a 9-bp deletion (AAGAAGGAC) involving nucleotides 55-63 in exon 2 of the NCF2 gene, predicting elimination of lys19/lys20/asp21 from the NCF2 protein. The maternal allele also contained a C-to-T transition at nucleotide 1183 in exon 14, resulting in an arg395-to-trp mutation (R395W; 608515.0010). The mother was heterozygous for these mutations. The allele from the father had an IVS4DS+1G-A mutation (608515.0005).

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

From Invitae, SCV000956351.1

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

Description

This variant, c.55_63delAAGAAGGAC, results in the deletion of 3 amino acid(s) of the NCF2 protein (p.Lys19_Asp21del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (ExAC no frequency). This variant has been observed on the opposite chromosome (in trans) from other pathogenic variants in individuals affected with chronic granulomatous disease (PMID: 10498624, 10598813, 18625437). This finding is consistent with autosomal recessive inheritance, and suggests that this variant contributes to disease. ClinVar contains an entry for this variant (Variation ID: 2245). Experimental studies and prediction algorithms are not available for this variant, and the functional significance of the affected amino acid(s) is currently unknown. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

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

Last Updated: Feb 27, 2021

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