VCV000002240.2 - ClinVar

NM_000433.3(NCF2):c.[479A>T;481A>G]

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(1)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Pathogenic

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

This haplotype includes the following variants

NM_000433.3(NCF2):c.[479A>T;481A>G]

Other names: NCF2, LYS160GLU AND ASP161VAL
Functional consequence: -
Links: ClinGen: CA026909; OMIM: 608515.0002

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
NCF2		-	-	GRCh38 GRCh37	599	635

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type 2	Pathogenic (1)	no assertion criteria provided	Feb 24, 1997	RCV000002328.4

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Pathogenic (Feb 24, 1997)	no assertion criteria provided Method: literature only	GRANULOMATOUS DISEASE, CHRONIC, AUTOSOMAL RECESSIVE, 2 Affected status: not provided Allele origin: germline	OMIM Accession: SCV000022486.2 First in ClinVar: Apr 04, 2013 Last updated: Jul 11, 2020	Publications: PubMed (1) PubMed: 9070911 Comment on evidence: In the neutrophils of a patient with p67-phox-deficient chronic granulomatous disease (CGD2; 233710), Bonizzato et al. (1997) found that the NCF2 mRNA was present in … (more) In the neutrophils of a patient with p67-phox-deficient chronic granulomatous disease (CGD2; 233710), Bonizzato et al. (1997) found that the NCF2 mRNA was present in normal amount and size. Reverse transcription SSCP analysis followed by direct DNA sequencing identified a heterozygous double substitution: a 479A-T transversion, resulting in a lys160 to glu (K160E) substitution, and a 481A-G transition, resulting in an asp161 to val (D161V) substitution, both in exon 5 of the NCF2 gene. This was a double nonconservative amino acid change. The nature of the mutation on the other allele was not identified. (less)

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Identification of a double mutation (D160V-K161E) in the p67phox gene of a chronic granulomatous disease patient.	Bonizzato A	Biochemical and biophysical research communications	1997	PMID: 9070911

Text-mined citations for this variant ...

Record last updated Jan 26, 2024

ClinVar Genomic variation as it relates to human health

NM_000433.3(NCF2):c.[479A>T;481A>G]

Variant Details

NM_000433.3(NCF2):c.[479A>T;481A>G]

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...