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

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
3 (Most recent: Mar 28, 2019)
Last evaluated:
Oct 20, 2018
Accession:
VCV000002245.4
Variation ID:
2245
Description:
9bp deletion
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NM_000433.3(NCF2):c.55_63del (p.Lys19_Asp21del)

Allele ID
17284
Variant type
Deletion
Variant length
9 bp
Cytogenetic location
1q25.3
Genomic location
1: 183590267-183590275 (GRCh38) GRCh38 UCSC
1: 183559402-183559410 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.183559406_183559414del
NC_000001.11:g.183590271_183590279del
NM_000433.3:c.55_63del NP_000424.2:p.Lys19_Asp21del
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000001.11:183590266:GTCCTTCTTGTCC:GTCC
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
dbSNP: rs796065033
ClinGen: CA212794
OMIM: 608515.0006
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 2 criteria provided, single submitter Oct 20, 2018 RCV000002333.5
Pathogenic 1 criteria provided, single submitter May 15, 2017 RCV000494542.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
NCF2 - - GRCh38
GRCh37
215 241

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(May 15, 2017)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000582904.4
Submitted: (Jan 29, 2019)
Evidence details
Comment:
The c.55_63delAAGAAGGAC variant has been published previously in association with CGD (Noack et al., 1999; Patiño et al., 1999; Yu et al., 2008). The variant … (more)
Likely pathogenic
(Oct 20, 2018)
criteria provided, single submitter
Method: clinical testing
Chronic granulomatous disease, autosomal recessive cytochrome b-positive, type 2
Allele origin: germline
Invitae
Accession: SCV000956351.1
Submitted: (Mar 28, 2019)
Evidence details
Publications
PubMed (3)
Comment:
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. … (more)
Pathogenic
(Oct 01, 1999)
no assertion criteria provided
Method: literature only
GRANULOMATOUS DISEASE, CHRONIC, AUTOSOMAL RECESSIVE, 2
Allele origin: germline
OMIM
Accession: SCV000022491.3
Submitted: (Dec 30, 2010)
Evidence details
Publications
PubMed (1)

Functional evidence

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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 this variant

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Title Author Journal Year Link
Focus on FOCIS: the continuing diagnostic challenge of autosomal recessive chronic granulomatous disease. Yu G Clinical immunology (Orlando, Fla.) 2008 PMID: 18625437
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 Human genetics 1999 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 Blood 1999 PMID: 10498624

Text-mined citations for rs796065033...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Feb 27, 2021