NM_000433.4(NCF2):c.482del (p.Lys161fs) AND Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type 2

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 26, 2018
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:: RCV000690026.6

Allele description [Variation Report for NM_000433.4(NCF2):c.482del (p.Lys161fs)]

NM_000433.4(NCF2):c.482del (p.Lys161fs)

Gene:

NCF2:neutrophil cytosolic factor 2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

1q25.3

Genomic location:

Preferred name:

NM_000433.4(NCF2):c.482del (p.Lys161fs)

HGVS:

NC_000001.11:g.183574507del
NG_007267.1:g.21076del
NM_000433.4:c.482delMANE SELECT
NM_001127651.3:c.482del
NM_001190789.2:c.366+3093del
NM_001190794.2:c.367-1214del
NP_000424.2:p.Lys161fs
NP_001121123.1:p.Lys161fs
LRG_88:g.21076del
NC_000001.10:g.183543641del
NC_000001.10:g.183543642del
NM_000433.3:c.482delA

Protein change:

K161fs

Links:

dbSNP: rs1558098982

NCBI 1000 Genomes Browser:

rs1558098982

Molecular consequence:

NM_000433.4:c.482del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001127651.3:c.482del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001190789.2:c.366+3093del - intron variant - [Sequence Ontology: SO:0001627]
NM_001190794.2:c.367-1214del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type 2
Synonyms:: CGD, AUTOSOMAL RECESSIVE CYTOCHROME b-POSITIVE, TYPE II; GRANULOMATOUS DISEASE, CHRONIC, DUE TO NCF2 DEFICIENCY; GRANULOMATOUS DISEASE, CHRONIC, AUTOSOMAL RECESSIVE, 2
Identifiers:: MONDO: MONDO:0009310; MedGen: C1856245; Orphanet: 379; OMIM: 233710

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000817702	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (May 26, 2018)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 10498624, 20167518, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000817702

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(May 26, 2018)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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

Hematologically important mutations: the autosomal recessive forms of chronic granulomatous disease (second update).

Roos D, Kuhns DB, Maddalena A, Bustamante J, Kannengiesser C, de Boer M, van Leeuwen K, Köker MY, Wolach B, Roesler J, Malech HL, Holland SM, Gallin JI, Stasia MJ.

Blood Cells Mol Dis. 2010 Apr 15;44(4):291-9. doi: 10.1016/j.bcmd.2010.01.009. Epub 2010 Feb 18. Review.

PubMed [citation]

PMID:: 20167518
PMCID:: PMC4568122

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV000817702.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Lys161Argfs*16) in the NCF2 gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has been reported as homozygous in an individual affected with chronic granulomatous disease (CGD) (PMID:¬†20167518). Loss-of-function variants in NCF2 are known to be pathogenic (PMID: 10498624, 20167518). For these reasons, this variant has been classified as Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 20, 2024

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